Simultaneous mapping of cathodoluminescence spectra and backscatter diffraction patterns in a scanning electron microscope.

Electron backscatter diffraction and cathodoluminescence are complementary scanning electron microscopy modes widely used in the characterisation of semiconductor films, respectively revealing the strain state of a crystalline material and the effect of this strain on the light emission from the sample. Conflicting beam, sample and detector geometries have meant it is not generally possible to acquire the two signals together during the same scan. Here, we present a method of achieving this simultaneous acquisition, by collecting the light emission through a transparent sample substrate. We apply this combination of techniques to investigate the strain field and resultant emission wavelength variation in a deep-ultraviolet micro-LED. For such compatible samples, this approach has the benefits of avoiding image alignment issues and minimising beam damage effects.

Metrology of crystal defects through intensity variations in secondary electrons from the diffraction of primary electrons in a scanning electron microscope.

Understanding defects and their roles in plastic deformation and device reliability is important for the development of a wide range of novel materials for the next generation of electronic and optoelectronic devices. We introduce the use of gaseous secondary electron detectors in a variable pressure scanning electron microscope for non-destructive imaging of extended defects using electron channelling contrast imaging. We demonstrate that all scattered electrons, including the secondary electrons, can provide diffraction contrast as long as the sample is positioned appropriately with respect to the incident electron beam. Extracting diffraction information through monitoring the modulation of the intensity of secondary electrons as a result of diffraction of the incident electron beam, opens up the possibility of performing low energy electron channelling contrast imaging to characterise low atomic weight and ultra-thin film materials. Our methodology can be adopted for large area, nanoscale structural characterisation of a wide range of crystalline materials including metals and semiconductors, and we illustrate this using the examples of aluminium nitride and gallium nitride. The capability of performing electron channelling contrast imaging, using the variable pressure mode, extends the application of this technique to insulators, which usually require conducting coatings on the sample surface for traditional scanning electron microscope based microstructural characterisation.

Determining GaN Nanowire Polarity and its Influence on Light Emission in the Scanning Electron Microscope.

The crystal polarity of noncentrosymmetric wurtzite GaN nanowires is determined nondestructively in the scanning electron microscope using electron backscatter diffraction (EBSD). The impact of the nanowire polarity on light emission is then investigated using cathodoluminescence (CL) spectroscopy. EBSD can determine polarity of noncentrosymmetric crystals by interrogating differences in the intensity distribution of bands of the EBSD pattern associated with semipolar planes. Experimental EBSD patterns from an array of GaN nanowires are compared with theoretical patterns produced using dynamical electron simulations to reveal whether they are Ga- or N-polar or, as in several cases, of mixed polarity. CL spectroscopy demonstrates the effect of the polarity on light emission, with spectra obtained from nanowires of known polarity revealing a small but measurable shift (≈28 meV) in the GaN near band edge emission energy between those with Ga and N polarity. We attributed this energy shift to a difference in impurity incorporation in nanowires of different crystal polarity. This approach can be employed to nondestructively identify polarity in a wide range of noncentrosymmetric nanoscale material systems and provide direct comparison with their luminescence.

Spatially-resolved optical and structural properties of semi-polar [Formula: see text] Al x Ga1-x N with x up to 0.56.

Pushing the emission wavelength of efficient ultraviolet (UV) emitters further into the deep-UV requires material with high crystal quality, while also reducing the detrimental effects of built-in electric fields. Crack-free semi-polar [Formula: see text] Al x Ga1-x N epilayers with AlN contents up to x = 0.56 and high crystal quality were achieved using an overgrowth method employing GaN microrods on m-sapphire. Two dominant emission peaks were identified using cathodoluminescence hyperspectral imaging. The longer wavelength peak originates near and around chevron-shaped features, whose density is greatly increased for higher contents. The emission from the majority of the surface is dominated by the shorter wavelength peak, influenced by the presence of basal-plane stacking faults (BSFs). Due to the overgrowth technique BSFs are bunched up in parallel stripes where the lower wavelength peak is broadened and hence appears slightly redshifted compared with the higher quality regions in-between. Additionally, the density of threading dislocations in these region is one order of magnitude lower compared with areas affected by BSFs as ascertained by electron channelling contrast imaging. Overall, the luminescence properties of semi-polar AlGaN epilayers are strongly influenced by the overgrowth method, which shows that reducing the density of extended defects improves the optical performance of high AlN content AlGaN structures.

Quantitative imaging of anti-phase domains by polarity sensitive orientation mapping using electron backscatter diffraction.

Advanced structural characterisation techniques which are rapid to use, non-destructive and structurally definitive on the nanoscale are in demand, especially for a detailed understanding of extended-defects and their influence on the properties of materials. We have applied the electron backscatter diffraction (EBSD) technique in a scanning electron microscope to non-destructively characterise and quantify antiphase domains (APDs) in GaP thin films grown on different (001) Si substrates with different offcuts. We were able to image and quantify APDs by relating the asymmetrical intensity distributions observed in the EBSD patterns acquired experimentally and comparing the same with the dynamical electron diffraction simulations. Additionally mean angular error maps were also plotted using automated cross-correlation based approaches to image APDs. Samples grown on substrates with a 4° offcut from the [110] do not show any APDs, whereas samples grown on the exactly oriented substrates contain APDs. The procedures described in our work can be adopted for characterising a wide range of other material systems possessing non-centrosymmetric point groups.

Diffraction effects and inelastic electron transport in angle-resolved microscopic imaging applications.

We analyse the signal formation process for scanning electron microscopic imaging applications on crystalline specimens. In accordance with previous investigations, we find nontrivial effects of incident beam diffraction on the backscattered electron distribution in energy and momentum. Specifically, incident beam diffraction causes angular changes of the backscattered electron distribution which we identify as the dominant mechanism underlying pseudocolour orientation imaging using multiple, angle-resolving detectors. Consequently, diffraction effects of the incident beam and their impact on the subsequent coherent and incoherent electron transport need to be taken into account for an in-depth theoretical modelling of the energy- and momentum distribution of electrons backscattered from crystalline sample regions. Our findings have implications for the level of theoretical detail that can be necessary for the interpretation of complex imaging modalities such as electron channelling contrast imaging (ECCI) of defects in crystals. If the solid angle of detection is limited to specific regions of the backscattered electron momentum distribution, the image contrast that is observed in ECCI and similar applications can be strongly affected by incident beam diffraction and topographic effects from the sample surface. As an application, we demonstrate characteristic changes in the resulting images if different properties of the backscattered electron distribution are used for the analysis of a GaN thin film sample containing dislocations.

Sucrose dependent mineral phosphate solubilization in Enterobacter asburiae PSI3 by heterologous overexpression of periplasmic invertases.

Enterobacter asburiae PSI3 solubilizes mineral phosphates in the presence of glucose by the secretion of gluconic acid generated by the action of a periplasmic pyrroloquinoline quinone dependent glucose dehydrogenase. In order to achieve mineral phosphate solubilization phenotype in the presence of sucrose, plasmids pCNK4 and pCNK5 containing genes encoding the invertase enzyme of Zymomonas mobilis (invB) and of Saccharomyces cerevisiae (suc2) under constitutive promoters were constructed with malE signal sequence (in case of invB alone as the suc2 is secreted natively). When introduced into E. asburiae PSI3, E. a. (pCNK4) and E. a. (pCNK5) transformants secreted 21.65 ± 0.94 and 22 ± 1.3 mM gluconic acid, respectively, in the presence of 75 mM sucrose and they also solubilized 180 ± 4.3 and 438 ± 7.3 µM P from the rock phosphate. In the presence of a mixture of 50 mM sucrose and 25 mM glucose, E. a. (pCNK5) secreted 34 ± 2.3 mM gluconic acid and released 479 ± 8.1 µM P. Moreover, in the presence of a mixture of eight sugars (10 mM each) in the medium, E. a. (pCNK5) released 414 ± 5.3 µM P in the buffered medium. Thus, this study demonstrates incorporation of periplasmic invertase imparted P solubilization ability to E. asburiae PSI3 in the presence of sucrose and mixture of sugars.

Artificial citrate operon confers mineral phosphate solubilization ability to diverse fluorescent pseudomonads.

Citric acid is a strong acid with good cation chelating ability and can be very efficient in solubilizing mineral phosphates. Only a few phosphate solubilizing bacteria and fungi are known to secrete citric acids. In this work, we incorporated artificial citrate operon containing NADH insensitive citrate synthase (gltA1) and citrate transporter (citC) genes into the genome of six-plant growth promoting P. fluorescens strains viz., PfO-1, Pf5, CHAO1, P109, ATCC13525 and Fp315 using MiniTn7 transposon gene delivery system. Comprehensive biochemical characterization of the genomic integrants and their comparison with plasmid transformants of the same operon in M9 minimal medium reveals the highest amount of ∼7.6±0.41 mM citric and 29.95±2.8 mM gluconic acid secretion along with ∼43.2±3.24 mM intracellular citrate without affecting the growth of these P. fluorescens strains. All genomic integrants showed enhanced citric and gluconic acid secretion on Tris-Cl rock phosphate (TRP) buffered medium, which was sufficient to release 200-1000 µM Pi in TRP medium. This study demonstrates that MPS ability could be achieved in natural fluorescent pseudomonads by incorporation of artificial citrate operon not only as plasmid but also by genomic integration.

Pseudomonas fluorescens ATCC 13525 containing an artificial oxalate operon and Vitreoscilla hemoglobin secretes oxalic acid and solubilizes rock phosphate in acidic alfisols.

Oxalate secretion was achieved in Pseudomonas fluorescens ATCC 13525 by incorporation of genes encoding Aspergillus niger oxaloacetate acetyl hydrolase (oah), Fomitopsis plaustris oxalate transporter (FpOAR) and Vitreoscilla hemoglobin (vgb) in various combinations. Pf (pKCN2) transformant containing oah alone accumulated 19 mM oxalic acid intracellularly but secreted 1.2 mM. However, in the presence of an artificial oxalate operon containing oah and FpOAR genes in plasmid pKCN4, Pf (pKCN4) secreted 13.6 mM oxalate in the medium while 3.6 mM remained inside. This transformant solubilized 509 µM of phosphorus from rock phosphate in alfisol which is 4.5 fold higher than the Pf (pKCN2) transformant. Genomic integrants of P. fluorescens (Pf int1 and Pf int2) containing artificial oxalate operon (plac-FpOAR-oah) and artificial oxalate gene cluster (plac-FpOAR-oah, vgb, egfp) secreted 4.8 mM and 5.4 mM oxalic acid, released 329 µM and 351 µM P, respectively, in alfisol. The integrants showed enhanced root colonization, improved growth and increased P content of Vigna radiata plants. This study demonstrates oxalic acid secretion in P. fluorescens by incorporation of an artificial operon constituted of genes for oxalate synthesis and transport, which imparts mineral phosphate solubilizing ability to the organism leading to enhanced growth and P content of V. radiata in alfisol soil.

2-ketogluconic acid secretion by incorporation of Pseudomonas putida KT 2440 gluconate dehydrogenase (gad) operon in Enterobacter asburiae PSI3 improves mineral phosphate solubilization.

Enterobacter asburiae PSI3 is known to efficiently solubilize rock phosphate by secretion of approximately 50 mM gluconic acid in Tris-buffered medium in the presence of 75 mM glucose and in a mixture of seven aldosugars each at 15 mM concentration, mimicking alkaline vertisol soils. Efficacy of this bacterium in the rhizosphere requires P release in the presence of low amount of sugars. To achieve this, E. asburiae PSI3 has been manipulated to express gluconate dehydrogenase (gad) operon of Pseudomonas putida KT 2440 to produce 2-ketogluconic acid. E. asburiae PSI3 harboring gad operon had 438 U of GAD activity, secreted 11.63 mM 2-ketogluconic and 21.65 mM gluconic acids in Tris-rock phosphate-buffered medium containing 45 mM glucose. E. asburiae PSI3 gad transformant solubilized 0.84 mM P from rock phosphate in TRP-buffered liquid medium. In the presence of a mixture of seven sugars each at 12 mM, the transformant brought about a drop in pH to 4.1 and released 0.53 mM P.

Repression of oxalic acid-mediated mineral phosphate solubilization in rhizospheric isolates of Klebsiella pneumoniae by succinate.

Two strains of Klebsiella (SM6 and SM11) were isolated from rhizospheric soil that solubilized mineral phosphate by secretion of oxalic acid from glucose. Activities of enzymes for periplasmic glucose oxidation (glucose dehydrogenase) and glyoxylate shunt (isocitrate lyase and glyoxylate oxidase) responsible for oxalic acid production were estimated. In presence of succinate, phosphate solubilization was completely inhibited, and the enzymes glucose dehydrogenase and glyoxylate oxidase were repressed. Significant activity of isocitrate lyase, the key enzyme for carbon flux through glyoxylate shunt and oxalic acid production during growth on glucose suggested that it could be inducible in nature, and its inhibition by succinate appeared to be similar to catabolite repression.

Rapid nondestructive analysis of threading dislocations in wurtzite materials using the scanning electron microscope.

We describe the use of electron channeling contrast imaging in the scanning electron microscope to rapidly and reliably image and identify threading dislocations (TDs) in materials with the wurtzite crystal structure. In electron channeling contrast imaging, vertical TDs are revealed as spots with black-white contrast. We have developed a simple geometric procedure which exploits the differences observed in the direction of this black-white contrast for screw, edge, and mixed dislocations for two electron channeling contrast images acquired from two symmetrically equivalent crystal planes whose g vectors are at 120° to each other. Our approach allows unambiguous identification of all TDs without the need to compare results with dynamical simulations of channeling contrast.

Plasmid load adversely affects growth and gluconic acid secretion ability of mineral phosphate-solubilizing rhizospheric bacterium Enterobacter asburiae PSI3 under P limited conditions.

Effect of the metabolic load caused by the presence of plasmids on mineral phosphate-solubilizing (MPS) Enterobacter asburiae PSI3, was monitored with four plasmid cloning vectors and one native plasmid, varying in size, nature of the replicon, copy number and antibiotic resistance genes. Except for one plasmid, the presence of all other plasmids in E. asburiae PSI3 resulted in the loss of the MPS phenotype as reflected by the failure to bring about a drop in pH and release soluble P when grown in media containing rock phosphate (RP) as the sole P source. When 100 µM soluble P was supplemented along with RP, the adverse effects of plasmids on MPS phenotype and on growth parameters was reduced for some plasmid bearing derivatives, as monitored in terms of specific growth rates, glucose consumed, gluconic acids yields and P released. When 10 mM of soluble P as the only P source, was added to the medium all transformants showed growth and pH drop comparable with native strain. It may be concluded that different plasmids impose, to varying extents, a metabolic load in the phosphate-solubilizing bacterium E. asburiae PSI3 and results in diminishing its growth and P-solubilizing ability in P deficient conditions.

Effect of transgenic rhizobacteria overexpressing Citrobacter braakii appA on phytate-P availability to mung bean plants.

Rhizosphere microorganisms possessing phytase activity are considered important for rendering phytate-P available to plants. In the present study, Citrobacter braakii phytase gene (appA) was over-expressed in rhizobacteria possessing plant growth promoting (PGP) traits for increasing their potential as bioinoculants. AppA was cloned under the lac promoter in the broad host-range expression vector pBBR1MCS2. Transformation of the recombinant construct pCBappA resulted in high constitutive phytase activity in all of the eight rhizobacterial strains belonging to genera Pantoea, Citrobacter, Enterobacter, Pseudomonas (two strains), Rhizobium (two strains) and Ensifer that were studied. Transgenic rhizobacterial strains were found to display varying level of phytase activity, ranging from 10 folds to 538 folds higher than the corresponding control strains. Transgenic derivative of Pseudomonas fluorescens CHA0, a well-characterized plant growth promoting rhizobacterium, showed highest expression of phytase (~8 U/ mg) activity in crude extracts. Although all transformants showed high phytase activity, rhizobacteria having ability to secrete organic acid, showed significantly higher release of P from Ca-phytate in buffered minimal media. AppA over-expressing rhizobacteria showed increased P content, dry weight (shoot) or shoot/ root ratio of mung bean (Vigna radiata) plants, to different extents, when grown in semi solid agar (SSA) medium containing Na-phytate or Ca-phytate as the P sources. This is the first report of over-expression of phytase in rhizobacterial strains and its exploitation for plant growth enhancement.

Broad-host-range plasmid-mediated metabolic perturbations in Pseudomonas fluorescens 13525.

Genetic engineering of fluorescent pseudomonads for various industrially, agriculturally and environmentally important bioprocesses often involves the use of suitable plasmids. Plasmid-mediated alterations in host physiology and metabolism are poorly understood for this group of organisms. Thus, we investigated the metabolic perturbations in Pseudomonas fluorescens 13525 due to the independent and combined presence of broad-host-range plasmids, pBBR1MCS-2 (copy number 30) and pUCPM18 derived pAB4 and pAB8 (copy number 14-16). Presence of pAB4 and pAB8 not only significantly increased the growth rate and glucose utilization of P. fluorescens 13525, but also increased glucose dehydrogenase activity and gluconic acid production indicating enhanced direct oxidative pathway for glucose catabolism. Additionally, increased secretion of pyruvic, acetic, and citric acids caused faster media acidification in presence of pAB4 and pAB8. Simultaneous presence of pAB4/pAB8 in Pf (pAB48) and pAB4/pBBR1MCS-2 in Pf (pAB4BBR1MCS-2) reduced their respective copy numbers to nearly half. Pf (pAB48) demonstrated further increase in direct oxidation pathway without altering growth and glucose depletion rates, as compared with single transformants. Conversely, pBBR1MCS-2 plasmid did not greatly alter P. fluorescens 13525 metabolism when present independently but masked the effects imposed by pAB4 when present in its combination. In conclusion, P. fluorescens 13525 redesigns its metabolism in response to the presence of plasmids irrespective of their nature, by enhancing anaplerosis with a simultaneous reduction in catabolism as indicated by increased pyruvate carboxylase and decreased citrate synthase activities, respectively. Such information will be helpful for vector designing during genetic engineering of fluorescent pseudomonads.

Heterologous expression of phosphoenolpyruvate carboxylase enhances the phosphate solubilizing ability of fluorescent pseudomonads by altering the glucose catabolism to improve biomass yield.

The Synechococcus elongatus PCC 6301 phosphoenolpyruvate carboxylase (ppc) gene was constitutively overexpressed in fluorescent pseudomonads, to increase the supply of oxaloacetate, a crucial anabolic precursor and an intermediate in biosynthesis of organic acids implicated in phosphate (P) solubilization. Pseudomonas fluorescens ATCC 13525, transformed with pAB3 plasmid containing the ppc gene showed a 14-fold increase in PPC activity under P-sufficiency resulting in increased carbon flow through the direct oxidative pathway and reduced metabolic overflow. Under P-limitation, contribution of the direct oxidative pathway significantly increased in P. fluorescens ATCC 13525; however, ppc overexpression enhanced glucose catabolism through intracellular phosphorylative pathway. These results correlated with gluconic, pyruvic and acetic acid levels as well as the activities of key glucose catabolic enzymes. Irrespective of the P-status, ppc overexpression improved biomass yield without altering growth rate, resulting in improved P- solubilizing abilities of P. fluorescens ATCC 13525 as well as of the wheat rhizosphere fluorescent pseudomonads isolates Fp585, P109 and Fp315. Collectively, ppc overexpression reversed the P-status dependent glucose distribution between the direct oxidative and phosphorylative pathways of glucose catabolism in P. fluorescens ATCC 13525 and presents a feasible genetic engineering approach for developing efficient P-solubilizing bacteria.

Metabolic channeling of glucose towards gluconate in phosphate-solubilizing Pseudomonas aeruginosa P4 under phosphorus deficiency.

Most phosphate-solubilizing bacteria (PSB), including the Pseudomonas species, release P from sparingly soluble mineral phosphates by producing high levels of gluconic acid from extracellular glucose, in a reaction catalyzed by periplasmic glucose dehydrogenase, which is an integral component of glucose catabolism of pseudomonads. To investigate the differences in the glucose metabolism of gluconic acid-producing PSB pseudomonads and low gluconic acid-producing/non-PSB strains, several parameters pertaining to growth and glucose utilization under P-sufficient and P-deficient conditions were monitored for the PSB isolate Pseudomonas aeruginosa P4 (producing approximately 46 mM gluconic acid releasing 437 microM P) and non-PSB P. fluorescens 13525. Our results show interesting differences in the channeling of glucose towards gluconate and other catabolic end-products like pyruvate and acetate with respect to P status for both strains. However, PSB strain P. aeruginosa P4, apart from exhibiting better growth under both low and high Pi conditions, differed from P. fluorescens 13525 in its ability to accumulate gluconate under P-solubilizing conditions. These alterations in growth, glucose utilization and acid secretion are correlated with glucose dehydrogenase, glucose-6-phosphate dehydrogenase and pyruvate carboxylase activities. The ability to shift glucose towards a direct oxidative pathway under P deficiency is speculated to underlie the differential gluconic acid-mediated P-solubilizing ability observed amongst pseudomonads.

In vivo restriction endonuclease activity of the Anabaena PCC 7120 XisA protein in Escherichia coli.

Anabaena PCC 7120 genome contains three elements, which get excised out during late stages of heterocyst differentiation by a site-specific recombination process. The XisA protein, which excises the nifD element, shows sequence homology with the integrase family of tyrosine recombinase. The 11 bp target site of XisA CGGAGTAATCC contains a 3 bp inverted repeat. Here, we report restriction endonuclease activity of XisA by specific loss of plasmids containing single or double target sites. The pMX25 plasmid containing two target sites demonstrated endonuclease activity proportional to excision frequency. Different plasmid substrates containing one base pair mutation in the inverted repeat of the target site were monitored for endonuclease activity. Mutation of A4C retained endonuclease activity, while other modifications lost endonuclease activity. The presence of an additional copy of the target site enhanced endonuclease activity. These results suggest that the XisA protein could be an IIE type of restriction endonuclease in addition to being a recombinase.