Relationships between microbial activity and soil physical and chemical properties in native and reforested Araucaria angustifolia forests in the state of São Paulo, Brazil

Araucaria angustifolia (Bert.) O. Kuntze is the main component of the Mixed Ombrophilous forest and, in the State of São Paulo, it is associated with a high diversity of soil organisms, essential for the maintenance of soil quality, making the conservation of this ecosystem a major and pressing challenge. The objective of this study was to identify the physical and chemical properties that are most closely correlated with dehydrogenase enzyme activity, basal respiration and microbial biomass under native (NF) and replanted (RF) Araucaria angustifolia forests in three regions of the state of São Paulo, in winter and summer. The main differentiating factors between the areas were also determined. Each forest was represented by three true replications; at each site, from around the araucaria trees, 15 soil samples (0-20 cm) were collected to evaluate the soil physical, chemical and microbiological properties. At the same points, forest litter was sampled to assess mass and chemical properties. The following microbiological properties were evaluated: microbial biomass carbon (MBC), basal respiration (CO2-C), metabolic quotient (Q: CO2), dehydrogenase enzyme activity (DHA) as well as the physical properties (moisture, bulk density, macroporosity and total porosity), soil chemical properties [pH, organic carbon (org-C), P, Ca, K, Mg, Al, H+Al], litter dry mass, and C, N and S contents. The data were subjected to analysis of variance (TWO-WAY: ANOVA). A Canonical Discriminant Analysis (CDA) and a Canonical Correlation Analysis (CCA) were also performed. In the soil under NF, the values of K, P, soil macroporosity, and litter dry mass were higher and Q: CO2 and DHA lower, regardless of the sampling period, and DHA was lower in winter. In the RF areas, the levels of moisture, porosity and Q: CO2 were higher in both sampling periods, and DHA was higher in winter. The MBC was only higher under NF in the summer, while the litter contents of C, N and S were greater in winter. In winter, CCA showed a high correlation of DHA with CO2-C, pH and H+Al, while in the summer org-C, moisture, Mg, pH and litter C were more associated with DHA and CO2-C. The CDA indicated H+Al, available P, total porosity, litter S content, and soil moisture as the most discriminating variables between NF and RF, but moisture was the most relevant, in both seasons and CO2-C only in winter. The combined analysis of CCA and CDA showed that the contribution of the microbiological variables to a differentiation of the areas was small at both samplings, which may indicate that the period after reforestation was long enough to allow an almost complete recovery of the microbial activity.

TCRep 3D: an automated in silico approach to study the structural properties of TCR repertoires.

TCRep 3D is an automated systematic approach for TCR-peptide-MHC class I structure prediction, based on homology and ab initio modeling. It has been considerably generalized from former studies to be applicable to large repertoires of TCR. First, the location of the complementary determining regions of the target sequences are automatically identified by a sequence alignment strategy against a database of TCR Vα and Vβ chains. A structure-based alignment ensures automated identification of CDR3 loops. The CDR are then modeled in the environment of the complex, in an ab initio approach based on a simulated annealing protocol. During this step, dihedral restraints are applied to drive the CDR1 and CDR2 loops towards their canonical conformations, described by Al-Lazikani et. al. We developed a new automated algorithm that determines additional restraints to iteratively converge towards TCR conformations making frequent hydrogen bonds with the pMHC. We demonstrated that our approach outperforms popular scoring methods (Anolea, Dope and Modeller) in predicting relevant CDR conformations. Finally, this modeling approach has been successfully applied to experimentally determined sequences of TCR that recognize the NY-ESO-1 cancer testis antigen. This analysis revealed a mechanism of selection of TCR through the presence of a single conserved amino acid in all CDR3β sequences. The important structural modifications predicted in silico and the associated dramatic loss of experimental binding affinity upon mutation of this amino acid show the good correspondence between the predicted structures and their biological activities. To our knowledge, this is the first systematic approach that was developed for large TCR repertoire structural modeling.

Chemical properties and mineralogy of soils with plinthite and petroplinthite in Iranduba (AM), Brazil

Large areas of Plinthosols with ferruginous materials such as plinthite and/or petroplinthite are fairly common in the Brazilian Amazon basin. This work was carried out to investigate the chemical behavior, mineralogical composition and weathering stage of four representative soil profiles with plinthite and petroplinthite, in Iranduba, AM (Central Amazon). Three well-drained soil profiles at high elevations were studied (P1, Plinthic Vetic Ferralsol; P2 and P3, Vetic Endopetric Plinthosol) and a contrasting poorly drained soil (P4 Haplic Plinthosol), located at low elevation. After profile descriptions, soil samples were collected from each horizon, air-dried, sieved (2 mm), and analyzed for particle-size distribution, pH, exchangeable cations (Al3+, Ca2+, Mg2+, K+, and Na+), as well as available P and total organic carbon (TOC) content. The minerals present in the clay and sand fractions, as well as in the ferruginous materials were identified by X-ray Diffraction (XRD). The weathering stage of these soils was assessed by means of Ki and Kr indexes, and the amounts of free and amorphous Fe and Al oxides by using dithionite citrate bicarbonate (DBC) and ammonium oxalate dissolution procedures, respectively. The results showed that all soils were extremely unfertile, with pH levels ranging between strong and moderate acidity, very low sum of bases and organic matter content, and of available P. The mineralogy of the soil profiles was very similar, mainly of the well-drained soils, with predominance of kaolinite and quartz in the clay and sand fractions, respectively. In the poorly-drained P4, 2:1 clay particles were also observed. These profiles can be considered highly developed according to the Ki index, however, the Ki value of P4 was higher, indicating that this soil was less developed than the others. In summary, these profiles with plinthite and petroplinthite can be characterized as highly developed and infertile soils and are, with exception of P4, well-drained.

Optimization of the sampling scheme for maps of physical and chemical properties estimated by kriging

The sampling scheme is essential in the investigation of the spatial variability of soil properties in Soil Science studies. The high costs of sampling schemes optimized with additional sampling points for each physical and chemical soil property, prevent their use in precision agriculture. The purpose of this study was to obtain an optimal sampling scheme for physical and chemical property sets and investigate its effect on the quality of soil sampling. Soil was sampled on a 42-ha area, with 206 geo-referenced points arranged in a regular grid spaced 50 m from each other, in a depth range of 0.00-0.20 m. In order to obtain an optimal sampling scheme for every physical and chemical property, a sample grid, a medium-scale variogram and the extended Spatial Simulated Annealing (SSA) method were used to minimize kriging variance. The optimization procedure was validated by constructing maps of relative improvement comparing the sample configuration before and after the process. A greater concentration of recommended points in specific areas (NW-SE direction) was observed, which also reflects a greater estimate variance at these locations. The addition of optimal samples, for specific regions, increased the accuracy up to 2 % for chemical and 1 % for physical properties. The use of a sample grid and medium-scale variogram, as previous information for the conception of additional sampling schemes, was very promising to determine the locations of these additional points for all physical and chemical soil properties, enhancing the accuracy of kriging estimates of the physical-chemical properties.

Wheat yield and physical properties of a brown latosol under no-tillage in south-central Paraná

Soil management influences the chemical and physical properties of soil. Chemical conditions have been thoroughly studied, while the role of soil physical conditions regarding crop yield has been neglected. This study aimed to analyze the wheat yield and its relationship with physical properties of an Oxisol under no-tillage (NT). The study was carried out between 2010 and 2011, in Reserva do Iguaçu, State of Paraná, Brazil, on the Campo Bonito farm, after 25 years of NT management. Based on harvest maps of barley (2006), wheat (2007) and maize (2009) of a plot (150 ha), zones with higher and lower yield potential (Z1 and Z2, respectively) were identified. Sampling grids with 16 units (50 x 50 m) and three sampling points per unit were established. The wheat grain yield (GY) and water infiltration capacity (WIC) were evaluated in 2010. Soil samples with disturbed and undisturbed structure were collected from the 0.00-0.10 and 0.10-0.20 m layers. The former were used to determine soil organic carbon (Corg) levels and the latter to determine soil bulk density (BD), total porosity (TP), macroporosity (Mac), and microporosity (Mic). Soil penetration resistance (PR) and water content (SWC) were also evaluated. The wheat GY of the whole plot was close to the regional average and the yield between the zones differed significantly, i.e. 22 % higher in Z1 than in Z2. No significant variation in Mic was observed between zones, but Z1 had higher Corg levels, SWC, TP and Mac and lower BD than Z2 in both soil layers, as well as a lower PR than Z2 in the 0.00-0.10 m layer. Therefore, soil physical conditions were more restrictive in Z2, in agreement with wheat yield and zone yield potential defined a priori, based on the harvest maps. Soil WIC in Z1 was significantly higher (30 %) than in Z2, in agreement with the results of TP and Mac which were also higher in Z1 in both soil layers. The correlation analysis of data of the two layers showed a positive relationship between wheat GY and the soil properties TP, SWC and WIC.

The effect of intrinsic soil properties on soil quality assessments

The assessment of soil quality is based on indicators and indices derived from soil properties. However, intrinsic soil properties may interfere with other soil properties that vary under different land uses and are used to calculate the indices. The aim of this study was to assess the extent to which intrinsic soil properties (clay and iron oxide contents) explain variable soil properties (sum of bases, potential acidity, organic carbon, total porosity, and bulk density) under different land uses (native forest, no-tillage and conventional agriculture) on small family farms in Southern Brazil. The results showed that the five properties evaluated can be included in soil quality assessments and are not influenced by the clay and iron oxide contents. It was concluded that for little weathered 1:1 and 2:1 phyllosilicate rich-soils, if the difference between the maximum and the minimum clay content under the different land uses is less than about 200 g kg-1 and the iron oxide content less than about 15 g kg-1, the physico-chemical soil properties in the surface layer are determined mostly by the land use.

Soil physical properties and grape yield influenced by cover crops and management systems

The use of cover crops in vineyards is a conservation practice with the purpose of reducing soil erosion and improving the soil physical quality. The objective of this study was to evaluate cover crop species and management systems on soil physical properties and grape yield. The experiment was carried out in Bento Gonçalves, RS, Southern Brazil, on a Haplic Cambisol, in a vineyard established in 1989, using White and Rose Niagara grape (Vitis labrusca L.) in a horizontal, overhead trellis system. The treatments were established in 2002, consisting of three cover crops: spontaneous species (SS), black oat (Avena strigosa Schreb) (BO), and a mixture of white clover (Trifolium repens L.), red clover (Trifolium pratense L.) and annual rye-grass (Lolium multiflorum L.) (MC). Two management systems were applied: desiccation with herbicide (D) and mechanical mowing (M). Soil under a native forest (NF) area was collected as a reference. The experimental design consisted of completely randomized blocks, with three replications. The soil physical properties in the vine rows were not influenced by cover crops and were similar to the native forest, with good quality of the soil structure. In the inter-rows, however, there was a reduction in biopores, macroporosity, total porosity and an increase in soil density, related to the compaction of the surface soil layer. The M system increased soil aggregate stability compared to the D system. The treatments affected grapevine yield only in years with excess or irregular rainfall.

Effects of tillage systems on physical properties of a cohesive yellow argisol in the northern state of Espírito Santo, Brazil

Tillage systems are a key element of the technology of crop production, both with a view to crop yield and from the perspective of soil conservation and sustainability of the production system. The aim of this paper was to evaluate the effects of five tillage systems on the physical properties of a cohesive Yellow Argisol. The experiment was installed in the field on January 21, 2011 and lasted 260 days, in an area previously used as pasture with Brachiaria grass without liming or fertilization, but irrigated by a low pressure spray system. The treatments, in five replications and in a randomized block design, consisted of: 1) disk plow (twice) + disk harrow + ridge-furrow tillage (raising a ridge along the planting row), 135 days after transplanting (DP + RID); 2) disk plow (twice) + disk harrow (DP no RID); 3) subsoiler (SB); 4) disk plow (twice) + disk harrow + scarification with three shanks along the plant row (DP + SPR); and 5) disk plow (twice) + disk harrow + scarification with three shanks in the total area (DP + STA). In all tillage systems, furrows were mechanically opened for the papaya plants. After the treatments, the mechanical resistance to penetration was determined, followed by soil moisture, mean weight diameter (MWD), geometric mean diameter (GMD), bulk density (BD), macroporosity (Ma), microporosity (Mi), and number of fruits per plant. There were differences in penetration resistance (PR) between treatments. The subsoiler was more effective to decrease RP to a distance of 0.35 m from the plants, perpendicular to the plant row. The scarifier resulted in a lower PR than DP or SB, even at the depth of 0.40 m, and it was more effective at greater distances perpendicular to the plant. All tillage systems induced a PR between 2.0 and 3.0 MPa at the depth with the highest concentration of papaya tree roots (0-0.25 m), improving the physical conditions to this depth. There was no statistical difference among the treatments for BD, Ma, Mi, MWD, and GMD at a depth of 0.20 m. The disk plow changed the physical properties of the soil most intensely to a depth of 0.20 m. The use of scarification, reduced tillage with a forest subsoiler, or ridge-furrow tillage did not improve the physical properties in the rhizosphere. Reduced tillage with a forest subsoiler resulted in a lower number of fruits per plant than all other treatments, which did not differ from each other.

Chemical and biological properties of phosphorus-fertilized soil under legume and grass cover (Cerrado region, Brazil)

The use of cover crops has been suggested as an effective method to maintain and/or increase the organic matter content, while maintaining and/or enhancing the soil physical, chemical and biological properties. The fertility of Cerrado soils is low and, consequently, phosphorus levels as well. Phosphorus is required at every metabolic stage of the plant, as it plays a role in the processes of protein and energy synthesis and influences the photosynthetic process. This study evaluated the influence of cover crops and phosphorus rates on soil chemical and biological properties after two consecutive years of common bean. The study analyzed an Oxisol in Selvíria (Mato Grosso do Sul, Brazil), in a randomized block, split plot design, in a total of 24 treatments with three replications. The plot treatments consisted of cover crops (millet, pigeon pea, crotalaria, velvet bean, millet + pigeon pea, millet + crotalaria, and millet + velvet bean) and one plot was left fallow. The subplots were represented by phosphorus rates applied as monoammonium phosphate (0, 60 and 90 kg ha-1 P2O5). In August 2011, the soil chemical properties were evaluated (pH, organic matter, phosphorus, potential acidity, cation exchange capacity, and base saturation) as well as biological variables (carbon of released CO2, microbial carbon, metabolic quotient and microbial quotient). After two years of cover crops in rotation with common bean, the cover crop biomass had not altered the soil chemical properties and barely influenced the microbial activity. The biomass production of millet and crotalaria (monoculture or intercropped) was highest. The biological variables were sensitive and responded to increasing phosphorus rates with increases in microbial carbon and reduction of the metabolic quotient.

Physical properties of a Red-Yellow Latosol and productivity of a signalgrass pasture fertilized with increasing nitrogen doses

The physical properties and fertility of the soil are important factors in the formation and establishment of pasture. Changes in physical properties affect the movement of water, air, nutrients and roots, which, in turn, affect the productivity and longevity of pastures. The objective of this study was to evaluate the physical properties of the soil and the dry matter yield of a pasture with signalgrass cv. Basilisk (Brachiaria decumbens cv. Basilisk), fertilized with increasing nitrogen doses (N), on a dystrophic Red-Yellow Latosol. The experiment was conducted on the Fazenda Rio Manso of the Universidade Federal dos Vales do Jequitinhonha e Mucuri, in Couto de Magalhães de Minas, State of Minas Gerais, Brazil. To evaluate the annual forage yield, a split plot scheme in a randomized block design with four replications was used, with N doses (0, 50, 100, 150, and 200 kg/ha/year) in the plots and growing seasons (first and second) in the subplots. For soil evaluation, a split plot scheme was used with N doses (0, 25, 50, 75 and 100 kg/ha/cut) in the plots and three sampling times (prior to the experiment, at the end of the first growing season and at the end of the second growing season) in the subplots in a randomized block design with four replications. This analysis was performed separately at two soil depths (0-3 and 10-13 cm). Forage samples were analyzed for the annual dry matter yield (DMY), and soil samples were analyzed for pre-consolidation pressure (σp), initial soil bulk density (Bd), total pore volume (TPV) and void index (Vd). Higher nitrogen doses increased the dry matter yield of signalgrass pasture and the pre-consolidation pressure of the soil. The total pore volume and void index decreased, and the initial soil bulk density increased, though without promoting soil compaction.

Influence of RF power on the properties of sputtered ZnO:Al thin films

Transparent conducting, aluminium doped zinc oxide thin films (ZnO:Al) were deposited by radio frequency (RF) magnetron sputtering. The RF power was varied from 60 to 350Wwhereas the substrate temperature was kept at 160 °C. The structural, electrical and optical properties of the as-deposited films were found to be influenced by the deposition power. The X-ray diffraction analysis showed that all the films have a strong preferred orientation along the [001] direction. The crystallite size was varied from 14 to 36 nm, however no significant change was observed in the case of lattice constant. The optical band gap varied in the range 3.44-3.58 eV. The lowest resistivity of 1.2×10 -3Vcm was shown by the films deposited at 250 W. The mobility of the films was found to increase with the deposition power.

Electrical and optical properties of Zn-In-Sn-O transparent conducting thin films

Indium tin oxide (ITO) is one of the widely used transparent conductive oxides (TCO) for application as transparent electrode in thin film silicon solar cells or thin film transistors owing to its low resistivity and high transparency. Nevertheless, indium is a scarce and expensive element and ITO films require high deposition temperature to achieve good electrical and optical properties. On the other hand, although not competing as ITO, doped Zinc Oxide (ZnO) is a promising and cheaper alternative. Therefore, our strategy has been to deposit ITO and ZnO multicomponent thin films at room temperature by radiofrequency (RF) magnetron co-sputtering in order to achieve TCOs with reduced indium content. Thin films of the quaternary system Zn-In-Sn-O (ZITO) with improved electrical and optical properties have been achieved. The samples were deposited by applying different RF powers to ZnO target while keeping a constant RF power to ITO target. This led to ZITO films with zinc content ratio varying between 0 and 67%. The optical, electrical and morphological properties have been thoroughly studied. The film composition was analysed by X-ray Photoelectron Spectroscopy. The films with 17% zinc content ratio showed the lowest resistivity (6.6 × 10 - 4 Ω cm) and the highest transmittance (above 80% in the visible range). Though X-ray Diffraction studies showed amorphous nature for the films, using High Resolution Transmission Electron Microscopy we found that the microstructure of the films consisted of nanometric crystals embedded in a compact amorphous matrix. The effect of post deposition annealing on the films in both reducing and oxidizing atmospheres were studied. The changes were found to strongly depend on the zinc content ratio in the films.

Sugarcane trash management assessed by the interaction of yield with soil properties

Currently, sugarcane plays an important global role, particularly with a view to alternative energy sources. Thus, in a sugarcane field of the mill Vale do Paraná S/A Álcool e Açúcar, Rubineia, São Paulo State, managed under two green cane harvest systems (cane trash left on and cane trash removed from the soil), Pearson and spatial correlations between the sugarcane yield (variety RB855035 in the third cut) and soil physical and chemical properties were studied to identify the property best correlated with stalk yield and the best harvest method. For this purpose, two geostatistical grids (121 sampling points on 1.30 ha) were installed on a eutrophic Red Argisol (homogeneous slope of 0.065 m m-1), in 2011, to determine the properties: stalk yield and sugarcane plant population, and soil resistance to penetration, gravimetric moisture, bulk density, and carbon stock, in the layers 0-0.20 and 0.20-0.40 m. The data were analyzed by descriptive, linear correlation and geostatistical analysis. In both treatments, the property stand density was best correlated with sugarcane yield (r = 0.725 in the trash mulching treatment - TM and r = 0.769 in the trash removal treatment - TR). However, in relation to the soil properties, bulk density (0-0.20 m) was best correlated (r = 0.305 in TM, r = 0.211 in TR). Similarly, from the spatial point of view, stand density was the property that best explained the sugarcane yield. However, in the TM treatment the density (0.20-0.40 m) was the only soil property spatially correlated with stalk yield. The carbon stock in the soil of the TM was 11.5 % higher than in the TR treatment. Results of the TM treatment were best, also with regard to soil management and conservation.

Substrate influence on the properties of doped thin silicon layers grown by Cat-CVD

We present structural and electrical properties for p- and n-type layers grown close to the transition between a-Si:H and nc-Si:H onto different substrates: Corning 1737 glass, ZnO:Al-coated glass and stainless steel. Structural properties were observed to depend on the substrate properties for samples grown under the same deposition conditions. Different behaviour was observed for n- and p-type material. Stainless steel seemed to enhance crystallinity when dealing with n-type layers, whereas an increased crystalline fraction was obtained on glass for p-type samples. Electrical conduction in the direction perpendicular to the substrate seemed to be mainly determined by the interfaces or by the existence of an amorphous incubation layer that might determine the electrical behaviour. In the direction perpendicular to the substrate, n-type layers exhibited a lower resistance value than p-type ones, showing better contact properties between the layer and the substrate.

Growth and magnetic properties of multiferroic LaxBi1-xMnO3 thin films

A comparative study of LaxBi1-xMnO3 thin films grown on SrTiO3 substrates is reported. It is shown that these films grow epitaxially in a narrow pressure-temperature range. A detailed structural and compositional characterization of the films is performed within the growth window. The structure and the magnetization of this system are investigated. We find a clear correlation between the magnetization and the unit-cell volume that we ascribe to Bi deficiency and the resultant introduction of a mixed valence on the Mn ions. On these grounds, we show that the reduced magnetization of LaxBi1-xMnO3 thin films compared to the bulk can be explained quantitatively by a simple model, taking into account the deviation from nominal composition and the Goodenough-Kanamori-Anderson rules of magnetic interactions.