Transcriptional profiling of Gram-positive Arthrobacter in the phyllosphere: induction of pollutant degradation genes by natural plant phenolic compounds.

Arthrobacter chlorophenolicus A6 is a Gram-positive, 4-chlorophenol-degrading soil bacterium that was recently shown to be an effective colonizer of plant leaf surfaces. The genetic basis for this phyllosphere competency is unknown. In this paper, we describe the genome-wide expression profile of A.chlorophenolicus on leaves of common bean (Phaseolus vulgaris) compared with growth on agar surfaces. In phyllosphere-grown cells, we found elevated expression of several genes known to contribute to epiphytic fitness, for example those involved in nutrient acquisition, attachment, stress response and horizontal gene transfer. A surprising result was the leaf-induced expression of a subset of the so-called cph genes for the degradation of 4-chlorophenol. This subset encodes the conversion of the phenolic compound hydroquinone to 3-oxoadipate, and was shown to be induced not only by 4-chlorophenol but also hydroquinone, its glycosylated derivative arbutin, and phenol. Small amounts of hydroquinone, but not arbutin or phenol, were detected in leaf surface washes of P.vulgaris by gas chromatography-mass spectrometry. Our findings illustrate the utility of genomics approaches for exploration and improved understanding of a microbial habitat. Also, they highlight the potential for phyllosphere-based priming of bacteria to stimulate pollutant degradation, which holds promise for the application of phylloremediation.

Leaf area of common bean genotypes during early pod filling as related to plant adaptation to limited phosphorus supply

Low phosphorus supply markedly limits leaf growth and genotypes able to maintain adequate leaf area at low P could adapt better to limited-P conditions. This work aimed to investigate the relationship between leaf area production of common bean (Phaseolus vulgaris) genotypes during early pod filling and plant adaptation to limited P supply. Twenty-four genotypes, comprised of the four growth habits in the species and two weedy accessions, were grown at two P level applied to the soil (20 and 80 mg kg-1) in 4 kg pots and harvested at two growth stages (pod setting and early pod filling). High P level markedly increased the leaf number and leaf size (leaf area per leaf), slightly increased specific leaf area but did not affect the net assimilation rate. At low P level most genotypic variation for plant dry mass was associated with leaf size, whereas at high P level this variation was associated primarily with the number of leaves and secondarily with leaf size, specific leaf area playing a minor role at both P level. Determinate bush genotypes presented a smaller leaf area, fewer but larger leaves with higher specific leaf area and lower net assimilation rate. Climbing genotypes showed numerous leaves, smaller and thicker leaves with a higher net assimilation rate. Indeterminate bush and indeterminate prostrate genotypes presented the highest leaf area, achieved through intermediate leaf number, leaf size and specific leaf area. The latter groups were better adapted to limited P. It is concluded that improved growth at low P during early pod filling was associated with common bean genotypes able to maintain leaf expansion through leaves with greater individual leaf area.

Rice grown in nutrient solution with doses of manganese and silicon

Although silicon is not recognized as a nutrient, it may benefit rice plants and may alleviate the Mn toxicity in some plant species. The dry matter yield (root, leaf, sheaths and leaf blade) and plant architecture (angle of leaf insertion and leaf arc) were evaluated in rice plants grown in nutrient solutions with three Mn doses, with and without Si addition. The treatments were arranged in a 2 x 3 factorial [with and without (2 mmol L-1) Si; three Mn doses (0.5; 2.5 and 10 µmol L-1)], in a randomized block design with 4 replications. The experimental unit was a 4 L plastic vase with 4 rice (Metica-1 cultivar) plants. Thirty nine days after keeping the seedlings in the nutrient solution the plant dry matter yield was determined; the angle of leaf insertion in the sheath and the leaf arc were measured; and the Si and Mn concentrations in roots, sheaths and leaves were determined. The analysis of variance (F test at 5 and 1 % levels) and the regression analysis (for testing plant response to Mn with the Si treatments) were performed. The Si added to the nutrient solution increased the dry matter yield of roots, sheaths and leaf blades and also decreased the angle of leaf blade insertion into the sheath and the foliar arc in the rice plant. Additionally, it ameliorated the rice plant architecture which allowed an increase in the dry matter yield. Similarly, the addition of Mn to the solution improved the architecture of the rice plants with gain in dry matter yield. As Si was added to the nutrient solution, the concentration of Mn in leaves decreased and in roots increased thus alleviating the toxic effects of Mn on the plants.

Role of sigmaB in the expression of Staphylococcus aureus cell wall adhesins ClfA and FnbA and contribution to infectivity in a rat model of experimental endocarditis.

Isogenic Staphylococcus aureus strains with different capacities to produce sigma(B) activity were analyzed for their ability to attach to fibrinogen- or fibronectin-coated surfaces or platelet-fibrin clots and to cause endocarditis in rats. In comparison to the sigma(B)-deficient strain, BB255, which harbors an rsbU mutation, both rsbU-complemented and sigma(B)-overproducing derivatives exhibited at least five times greater attachment to fibrinogen- and fibronectin-coated surfaces and showed increased adherence to platelet-fibrin clots. No differences in adherence were seen between BB255 and a DeltarsbUVWsigB isogen. Northern blotting analyses revealed that transcription of clfA, encoding fibrinogen-binding protein clumping factor A, and fnbA, encoding fibronectin-binding protein A, were positively influenced by sigma(B). Sigma(B) overproduction resulted in a statistically significant increase in positive spleen cultures and enhanced bacterial densities in both the aortic vegetations and spleens at 16 h postinoculation. In contrast, at 72 h postinoculation, tissues infected with the sigma(B) overproducer had lower bacterial densities than did those infected with BB255. These results suggest that although sigma(B) appears to increase the adhesion of S. aureus to various host cell-matrix proteins in vitro, it has limited effect on pathogenesis in the rat endocarditis model. Sigma(B) appears to have a transient enhancing effect on bacterial density in the early stages of infection that is lost during progression.

Microbial biomass and activity in litter during the initial development of pure and mixed plantations of Eucalyptus grandis and Acacia mangium

Studies on microbial activity and biomass in forestry plantations often overlook the role of litter, typically focusing instead on soil nutrient contents to explain plant and microorganism development. However, since the litter is a significant source of recycled nutrients that affect nutrient dynamics in the soil, litter composition may be more strongly correlated with forest growth and development than soil nutrient contents. This study aimed to test this hypothesis by examining correlations between soil C, N, and P; litter C, N, P, lignin content, and polyphenol content; and microbial biomass and activity in pure and mixed second-rotation plantations of Eucalyptus grandis and Acacia mangium before and after senescent leaf drop. The numbers of cultivable fungi and bacteria were also estimated. All properties were correlated with litter C, N, P, lignin and polyphenols, and with soil C and N. We found higher microbial activity (CO2 evolution) in litter than in soil. In the E. grandis monoculture before senescent leaf drop, microbial biomass C was 46 % higher in litter than in soil. After leaf drop, this difference decreased to 16 %. In A. mangium plantations, however, microbial biomass C was lower in litter than in soil both before and after leaf drop. Microbial biomass N of litter was approximately 94 % greater than that of the soil in summer and winter in all plantations. The number of cultivable fungi and bacteria increased after leaf drop, especially so in the litter. Fungi were also more abundant in the E. grandis litter. In general, the A. mangium monoculture was associated with higher levels of litter lignin and N, especially after leaf drop. In contrast, the polyphenol and C levels in E. grandis monoculture litter were higher after leaf drop. These properties were negatively correlated with total soil C and N. Litter in the mixed stands had lower C:N and C:P ratios and higher N, P, and C levels in the microbial biomass. This suggests more effective nutrient cycling in mixed plantations in the long term, greater stimulation of microbial activity in litter and soil, and a more sustainable system in general.

Soil infiltration based on bp neural network and grey relational analysis

Soil infiltration is a key link of the natural water cycle process. Studies on soil permeability are conducive for water resources assessment and estimation, runoff regulation and management, soil erosion modeling, nonpoint and point source pollution of farmland, among other aspects. The unequal influence of rainfall duration, rainfall intensity, antecedent soil moisture, vegetation cover, vegetation type, and slope gradient on soil cumulative infiltration was studied under simulated rainfall and different underlying surfaces. We established a six factor-model of soil cumulative infiltration by the improved back propagation (BP)-based artificial neural network algorithm with a momentum term and self-adjusting learning rate. Compared to the multiple nonlinear regression method, the stability and accuracy of the improved BP algorithm was better. Based on the improved BP model, the sensitive index of these six factors on soil cumulative infiltration was investigated. Secondly, the grey relational analysis method was used to individually study grey correlations among these six factors and soil cumulative infiltration. The results of the two methods were very similar. Rainfall duration was the most influential factor, followed by vegetation cover, vegetation type, rainfall intensity and antecedent soil moisture. The effect of slope gradient on soil cumulative infiltration was not significant.

Nucleation of diamond on silicon, SiAlON, and graphite substrates coated with an a-C:H layer

We investigated the influence of a hydrogenated disordered carbon (a-C:H) layer on the nucleation of diamond. Substrates c-Si<100>, SiAlON, and highly oriented pyrolytic graphite {0001} were used in this study. The substrate surfaces were characterized with Auger electron spectroscopy (AES) while diamond growth was followed with Raman spectroscopy and scanning electron microscopy (SEM). It was found that on silicon and SiAlON substrates the presence of the a-C:H layer enabled diamond to grow readily without any polishing treatment. Moreover, more continuous diamond films could be grown when the substrate was polished with diamond powder prior to the deposition of the a-C:H layer. This important result suggests that the nucleation of diamond occurs readily on disordered carbon surfaces, and that the formation of this type of layer is indeed one step in the diamond nucleation mechanism. Altogether, the data refute the argument that silicon defects play a direct role in the nucleation process. Auger spectra revealed that for short deposition times and untreated silicon surfaces, the deposited layer corresponds to an amorphous carbon layer. In these cases, the subsequent diamond nucleation was found to be limited. However, when the diamond nucleation density was found to be high; i.e., after lengthy deposits of a¿C:H or after diamond polishing, the Auger spectra suggested diamondlike carbon layers.

Ammonia volatilization and yield components after application of polymer-coated urea to maize

A form of increasing the efficiency of N fertilizer is by coating urea with polymers to reduce ammonia volatilization. The aim of this study was to evaluate the effect of polymer-coated urea on the control of ammonia volatilization, yield and nutritional characteristics of maize. The experiment was carried out during one maize growing cycle in 2009/10 on a Geric Ferralsol, inUberlândia, MG, Brazil. Nitrogen fertilizers were applied as topdressing on the soil surface in the following urea treatments: polymer-coated urea at rates of 45, 67.5 and 90 kg ha-1 N and one control treatment (no N), in randomized blocks with four replications. Nitrogen application had a favorable effect on N concentrations in leaves and grains, Soil Plant Analysis Development (SPAD) chlorophyll meter readings and on grain yield, where as coated urea had no effect on the volatilization rates, SPAD readings and N leaf and grain concentration, nor on grain yield in comparison to conventional fertilization.

Physiological and morphological responces of Brachiaria spp. to flooding

The physiological and morphological responses of the forage grasses Brachiaria brizantha cv. Marandu, B. decumbens and B. humidicola were compared for plants grown in pots under flooding and well-drained conditions for 14 days. Flooding reduced specific leaf area and biomass allocation to roots in all species and enhanced leaf senescence in B. brizantha and B. decumbens. Relative growth rate was reduced by flooding in B. brizantha and B. decumbens, but not in B. humidicola.Leaf elongation rate was unaffected by flooding in B. decumbens and B. humidicola, but declined in B. brizantha since the first day of flooding. Net photosynthesis and leaf chlorophyll content were reduced by flooding in B. brizantha; however, no flooding effect could be detected in the other two species. For all species, there was a close relationship between net photosynthesis and stomatal conductance under flooding. These results show that the studied species have distinct degrees of tolerance to flood, B. brizantha is intolerant, B. decumbens is moderately tolerant and B. humidicola is tolerant. Because leaf elongation rate was immediately depressed by flooding only in B. brizantha, this measurement could be appropriate as an early detection mechanism for relative flood tolerance in Brachiaria spp.

Whitefly, aphids and thrips attack on cabbage

The objective of this work was to investigate the relationships between predators and parasitoids, leaf chemical composition, levels of leaf nitrogen and potassium, total rainfall, relative humidity, daylight and median temperature on the intensity of whitefly, aphid, and thrips attack on cabbage. Whitefly, aphids and thrips population tended to proliferate in the final stage of plant or reached a peak population about 40 days after plantation. The whitefly and thrips tended to increase with an increase in the median temperature. A dependence of Cheiracanthium inclusum and Adialytus spp. populations on whitefly and aphids populations, respectively, was observed. No significant effect was detected between K and nonacosane leaf content and aphid population. However, an increase in leaf N content was followed by a decrease of this insect population. No significant relation was observed between leaf N, K and nonacosane and whitefly and thrips populations. Highest nonacosane levels were observed in plants 40 days after transplant, and relative humidity correlated negatively with nonacosane. Natural enemies, especially the parasitoid Adialytus spp. and the spiders can be useful controlling agents of the whitefly and aphids in cabbage. Median temperature can increase whitefly and thrips populations.

Maize leaf development under climate change scenarios

The objective of this work was to simulate maize leaf development in climate change scenarios at Santa Maria, RS, Brazil, considering symmetric and asymmetric increases in air temperature. The model of Wang & Engel for leaf appearance rate (LAR), with genotype-specific coefficients for the maize variety BRS Missões, was used to simulate tip and expanded leaf accumulated number from emergence to flag leaf appearance and expansion, for nine emergence dates from August 15 to April 15. LAR model was run for each emergence date in 100-year climate scenarios: current climate, and +1, +2, +3, +4 and +5°C increase in mean air temperature, with symmetric and asymmetric increase in daily minimum and maximum air temperature. Maize crop failure due to frost decreased in elevated temperature scenarios, in the very early and very late emergence dates, indicating a lengthening in the maize growing season in warmer climates. The leaf development period in maize was shorter in elevated temperature scenarios, with greater shortening in asymmetric temperature increases, indicating that warmer nights accelerate vegetative development in maize.

Growth of lulo (Solanum quitoense Lam.) plants affected by salinity and substrate

The effects of 0, 30 and 60 mM NaCl and substrates (red peat, sand or 3:1:1 [w/w] mixture of peat, sand, or soil) on vegetative growth of lulo, an Andean fruit species, during 12 weeks were studied. The experiment was carried out by using 2000 cm³ of polypropylene plastic pots under greenhouse conditions. Plant height, number of leaves and nodes, leaf area, total plant dry matter (DM), and shoot/root ratio were evaluated. With the increase of salt concentration, the plant height, the number of leaves and nodes, the leaf areas and plant dry mass DM decreased, whereas shoot/root ratio increased. Sand grown lulo plants were most affected by salinity and presented total mortality at 60 mM NaCl. On the other hand, plants held either in peat or in substrate mixture developed larger height, greater leaf and node numbers, higher leaf area and dry matter content. Shoot/root ratio in control (soil) and sand-grown plants (30 mM NaCl) was lower.

Lidar measurement of surface melt for a temperate Alpine glacier at the seasonal and hourly scales

This study shows how a new generation of terrestrial laser scanners can be used to investigate glacier surface ablation and other elements of glacial hydrodynamics at exceptionally high spatial and temporal resolution. The study area is an Alpine valley glacier, Haut Glacier d'Arolla, Switzerland. Here we use an ultra-long-range lidar RIEGL VZ-6000 scanner, having a laser specifically designed for measurement of snow- and ice-cover surfaces. We focus on two timescales: seasonal and daily. Our results show that a near-infrared scanning laser system can provide high-precision elevation change and ablation data from long ranges, and over relatively large sections of the glacier surface. We use it to quantify spatial variations in the patterns of surface melt at the seasonal scale, as controlled by both aspect and differential debris cover. At the daily scale, we quantify the effects of ogive-related differences in ice surface debris content on spatial patterns of ablation. Daily scale measurements point to possible hydraulic jacking of the glacier associated with short-term water pressure rises. This latter demonstration shows that this type of lidar may be used to address subglacial hydrologic questions, in addition to motion and ablation measurements.

Timing and nature of alluvial fan and strath terrace formation in the Eastern Precordillera of Argentina

Sixty-eight 10Be terrestrial cosmogenic nuclide (TCN) surface exposure ages are presented to define the timing of alluvial fan and strath terrace formation in the hyper-arid San Juan region of the Argentine Precordillera. This region is tectonically active, and numerous fault scarps traverse Quaternary landforms. The three study sites, Marquesado strath complex, Loma Negra alluvial fan and Carpintería strath complex reveal a history of alluvial fan and strath terrace development over the past w225 ka. The Marquesado complex Q3m surface dates to w17 3 ka, whereas the Loma Negra Q1ln, Q2ln, Q3ln, Q4ln, and Q5ln surfaces date to w24 3 ka, w48 2 ka, w65 13 ka, w105 21 ka, and w181 29 ka, respectively. The Carpintería complex comprises eight surfaces that have been dated and include the Q1c (w23 3 ka), Q2c (w5 5 ka), Q3ac (w25 12 ka), Q3bc (w29 15 ka), Q4c (w61 12 ka), Q5c (w98 18 ka), Q6c (w93 18 ka), and Q7c (w212 37 ka). 10Be TCN depth profile data for the Loma Negra alluvial fan complex and Carpintería strath terrace complex, as well as OSL ages on some Carpintería deposits, aid in refining surface ages for comparison with local and global climate proxies, and additionally offer insights into inheritance and erosion rate values for TCNs (w10 104 10Be atoms/g of SiO2 and w5 m Ma 1, respectively). Comparison with other alluvial fan studies in the region show that less dynamic and older preserved surfaces occur in the Carpintería and Loma Negra areas with only younger alluvial fan surfaces preserved both to the north and south. These data in combination with that of other studies illustrate broad regional agreement between alluvial fan and strath terrace ages, which suggests that climate is the dominant forcing agent in the timing of terrace formation in this region.

Accounting for adsorption and desorption in Lattice Boltzmann simulations

We report a Lattice-Boltzmann scheme that accounts for adsorption and desorption in the calculation of mesoscale dynamical properties of tracers in media of arbitrary complexity. Lattice Boltzmann simulations made it possible to solve numerically the coupled Navier-Stokes equations of fluid dynamics and Nernst-Planck equations of electrokinetics in complex, heterogeneous media. With the moment propagation scheme, it became possible to extract the effective diffusion and dispersion coefficients of tracers, or solutes, of any charge, e.g., in porous media. Nevertheless, the dynamical properties of tracers depend on the tracer-surface affinity, which is not purely electrostatic and also includes a species-specific contribution. In order to capture this important feature, we introduce specific adsorption and desorption processes in a lattice Boltzmann scheme through a modified moment propagation algorithm, in which tracers may adsorb and desorb from surfaces through kinetic reaction rates. The method is validated on exact results for pure diffusion and diffusion-advection in Poiseuille flows in a simple geometry. We finally illustrate the importance of taking such processes into account in the time-dependent diffusion coefficient in a more complex porous medium.