Burial Of Residues Research Articles

Less efficient residue‐derived soil organic carbon formation under no‐till irrigated corn

AbstractSoil organic carbon (SOC) stores a large portion of terrestrial C, yet the mechanisms that affect its formation efficiency under different residue management in irrigated systems are still not well understood. No‐till (NT) increases SOC concentrations in topsoil compared with conventional tillage (CT) but there is uncertainty surrounding the stability of these gains in irrigated systems. We investigated the effect of NT and CT residue management on CO2 loss and SOC formation by applying isotopically (13C) labeled residues on the surface or incorporated in the mineral soil of disturbed (i.e., CT) or undisturbed (i.e., NT) soil in a semiarid, NT, sprinkler‐irrigated, continuous corn (Zea mays L.) field. We measured residue‐derived C in CO2, bulk soil, dissolved organic C, particulate organic matter (POM), and silt‐ and clay‐sized mineral‐associated organic matter (MAOM) fractions. Twelve months after residue addition, soils with surface‐applied residue produced 19% more CO2 and formed 41% less SOC than residue‐incorporated soils. Across all treatments, 62% of residue‐derived C was recovered in POM, and 38% in the MAOM fractions. Residue‐derived bulk soil C formation was more efficient when the residue was incorporated (0.60) rather than surface‐applied (0.42), suggesting that mixing and burial of residue within the soil matrix is a key pathway of SOC formation. During the growing season, surface residue under NT management in irrigated systems is particularly vulnerable to decomposition and will require additional conservation strategies to generate long‐term C sequestration.

Plough section control for optimised uniformity in primary tillage

Primary tillage is in many cases crucial for successful crop establishment and weed and pest control. Inversion tillage using a mouldboard plough may be required when a uniform ploughing operation covering the entire field is preferred. The ploughing operation is especially challenging at the interface area between headlands and the main cropping area. Overlapping at the interface causes a mixing of the topsoil, rather than a soil inversion, and poor burial of residues and weeds, especially of concern in organic farming. The aim of the research was to study novel plough section control designs to optimise the interface area. Concept designs with hydraulic control were studied and the preferred was developed and tested in real field operations. The research concluded that the concept was functional and by visual inspection the interface was optimised. In addition, the section control can improve operations in irregularly shaped fields.

Management of forest harvest residues affects soil nutrient availability during reforestation of Eucalyptus grandis

Maintaining Eucalyptus harvest residues on site contributes to forest soil productivity and system sustainability, but in temperate climate slow decomposition of residues left on the soil surface limits the amounts of recycled nutrients available for future reforestation. In this work, decomposition rates (k) of the different fractions of Eucalyptus grandis residues left on the soil surface or incorporated into the soil (buried) by tillage were quantified. Thus, the potential rate of nutrient release was determined for N, P, K, Ca, Mg, and the effect on the growth of E. grandis after reforestation. Biomass decomposition and nutrient release profiles (3, 6, 9, 12, 18, 24 and 30 months) were determined for both left on soil surface and buried residues. Tree diameter at breast height (DBH), total height, and nutrient content in leaves were determined in young trees. Each buried residue had a higher k than the corresponding left on soil surface residue with 79 and 47 % biomass loss, respectively. On average, the effect of burial decreased decomposition half-lives from 3.5 to 1.2 years. Potassium recycling was rapid through the period, while Ca release (bark, branches) increased in the last 6 months. Residue burial increased N, P, K, Ca and Mg release by 22, 26, 5, 20 and 13 %, respectively; in addition, it improved soil quality by both increasing exchangeable cations and decreasing soil acidity. Although Ca and Mg concentrations in leaves after reforestation (second turn plantation) increased with residue incorporation, the treatment with residue removal presented significantly higher DBH and height.

Long-term tillage impacts on soil organic matter components and related properties on a Typic Argiudoll

Soil organic matter affects a number of soil processes and properties. A better understanding of soil-profile distribution of organic matter components and related soil properties under long-term tillage systems is thus needed. The objective of this study was to evaluate the impacts of 33 years no-till (NT), double disk (DD), chisel (CH), and plow tillage (PT) under corn (Zea mays L.)–soybean (Glycine max L.) rotation on soil organic C (SOC), particulate organic matter (POM), pH, and wet aggregate stability to 100cm soil depth on a Sharpsburg silty clay loam (fine, montmorillonitic, mesic Typic Argiudolls) in eastern NE. After 33 years, NT and DD management increased SOC by 1.2 times and mean weight diameter (MWD) of aggregates by 2 times compared with CH and PT at the 0–10cm depth. At the 0–20cm, NT had 1.1 times higher SOC concentration than CH and PT. When compared with data collected 24 years prior to this study, SOC at the 0–20cm increased by 12.5% across NT, DD, and CH and by 2.7% for PT. No-till had 5 times higher total POM concentration than PT, 4.7 times higher than CH, and 2.4 times higher than DD at the 0–10cm depth. However, at the 10–20cm, PT had higher POM than other tillage systems, which is most probably due to mixing and burial of residues at the bottom of the plow layer. Soil pH did not differ among tillage treatments at the 0–10cm, but it differed in this order: PT>CH>DD>NT at the 10–20cm and PT=CH=DD>NT at the 20–40cm depth. The lower pH under NT, DD, and CH in deeper soil depths may be due to the limited or no lime mixing in these systems compared with PT. When compared with data (pH 5) collected 33 years prior to this study, soil pH increased by 0.9 in NT, 1.4 in DD, 1.5 in CH, and 1.9 units in PT at 0–20cm depth, probably due to surface application and incorporation of lime. Overall, 33 years of NT increased near-surface soil organic matter components and soil aggregation compared with the PT.

A Protein Solvation Model Based on Residue Burial.

The influence of solvent on the individual amino acids of a protein depends not simply on their surface exposure but rather on the degree of their burial within the structure. This property can be related to a simple geometrical measure termed circular variance. Circular variance depends on the spatial distribution of neighboring residues and varies from zero to one as a residue becomes buried. Its only adjustable parameter is a cutoff distance for selecting neighbors. Here, we show that circular variance can be used to build a fast and effective model of protein solvation energies. For this, we combine a coarse-grain protein representation with statistical potentials derived by Boltzmann inversion of circular variance probability distributions for different classes of pseudoatom within a large protein structure database. The method is shown to work well for distinguishing native protein structures from decoy structures generated in a variety of ways. It can also be used to detect specific residues in unfavorable solvent environments. Compared to surface accessibility, circular variance calculations are faster, less sensitive to small conformational changes, and able to account for the longer-range interactions that characterize the electrostatic component of solvent effects. The resulting solvation energies can be used alone or as part of a more general coarse-grain protein model.

Energetics of Hydrogen Bond Switch, Residue Burial and Cavity Analysis Reveals Molecular Basis of Improved Heparin Binding to Antithrombin

Antithrombin III (ATIII) is the main inhibitor of the coagulation proteases like factor Xa and thrombin. Anticoagulant activity of ATIII is increased by several thousand folds when activated by vascular wall heparan sulfate proteoglycans (HSPGs) and pharmaceutical heparins. ATIII isoforms in human plasma, alpha-ATIII and beta-ATIII differ in the amount of glycosylation which is the basis of differences in their heparin binding affinity and function. Crystal structures and site directed mutagenesis studies have mapped the heparin binding site in ATIII, however the hydrogen bond switch and energetics of interaction during the course of heparin dependent conformational change remains largely unclear. An analysis of heparin bound conformational states of ATIII using PEARLS software showed that in heparin bound intermediate state, Arg 47 and Arg 13 residues make hydrogen bonds with heparin but in the activated conformation Lys 11 and Lys 114 have more hydrogen bond interactions. In the protease bound-antithrombin-pentasaccharide complex Lys 114, Pro 12 and Lys 125 form important hydrogen bonding interactions. The results showed that A-helix and N-terminal end residues are more important in the initial interactions but D-helix is more important during the latter stage of conformational activation and during the process of protease inhibition. We carried out the residue wise Accessible Surface Area (ASA) analysis of alpha and beta ATIII native states and the results indicated major differences in burial of residues from Ser 112 to Ser 116 towards the N-terminal end. This region is involved in the P-helix formation on account of heparin binding. A cavity analysis showed a progressively larger cavity formation during activation in the region just adjacent to the heparin binding site towards the C-terminal end. We hypothesize that during the process of conformational change after heparin binding beta form of antithrombin has low energy barrier to form D-helix extension toward N and C-terminal end as compared to alpha isoform.

The Histamine N-Methyltransferase T105I Polymorphism Affects Active Site Structure and Dynamics

Histamine N-methyltransferase (HNMT) is the primary enzyme responsible for inactivating histamine in the mammalian brain. The human HNMT gene contains a common threonine-isoleucine polymorphism at residue 105, distal from the active site. The 105I variant has decreased activity and lower protein levels than the 105T protein. Crystal structures of both variants have been determined but reveal little regarding how the T105I polymorphism affects activity. We performed molecular dynamics simulations for both 105T and 105I at 37 degrees C to explore the structural and dynamic consequences of the polymorphism. The simulations indicate that replacing Thr with the larger Ile residue leads to greater burial of residue 105 and heightened intramolecular interactions between residue 105 and residues within helix alpha3 and strand beta3. This altered, tighter packing is translated to the active site, resulting in the reorientation of several cosubstrate-binding residues. The simulations also show that the hydrophobic histamine-binding domain in both proteins undergoes a large-scale breathing motion that exposes key catalytic residues and lowers the hydrophobicity of the substrate-binding site.

Design of temperature-sensitive mutants solely from amino acid sequence.

Temperature-sensitive (Ts) mutants are a powerful tool with which to study gene function in vivo. Ts mutants are typically generated by random mutagenesis followed by laborious screening procedures. By using the Escherichia coli cytotoxin CcdB as a model system, simple procedures for generating Ts mutants at high frequency through site-directed mutagenesis were developed. Putative buried, hydrophobic residues are selected through analysis of the protein sequence. Residue burial is confirmed by ensuring that substitution of the residue by Asp leads to protein inactivation. At such sites, a Ts phenotype can typically be generated either by (i) substitution of two predicted, buried residues with the 18 remaining amino acids or (ii) introduction of Lys, Ser, Ala, and Trp at three to four predicted buried sites. By using these design strategies, 17 tight Ts mutants of CcdB were isolated at four predicted buried sites. The rules were further verified by making several Ts mutants of yeast Gal4 at residues 68, 69, and 70. No Ts mutants of either protein have been previously reported. Such Ts mutants of Gal4 can be used for conditional expression of a variety of genes by using the well characterized upstream-activating-sequence-Gal4 system.

Quantifying the effect of burial of amino acid residues on protein stability.

The average contribution of individual residue to folding stability and its dependence on buried accessible surface area (ASA) are obtained by two different approaches. One is based on experimental mutation data, and the other uses a new knowledge-based atom-atom potential of mean force. We show that the contribution of a residue has a significant correlation with buried ASA and the regression slopes of 20 amino acid residues (called the buriability) are all positive (pro-burial). The buriability parameter provides a quantitative measure of the driving force for the burial of a residue. The large buriability gap observed between hydrophobic and hydrophilic residues is responsible for the burial of hydrophobic residues in soluble proteins. Possible factors that contribute to the buriability gap are discussed.

Tillage effects on barley residue cover during fallow in semiarid Aragon

Maintenance of crop residues on the soil surface is considered the most effective method to control wind erosion. In semiarid Aragon (NE Spain), where the risk of wind erosion can be high, the adoption of conservation tillage systems has been encouraged as a fallow management alternative. However, little information concerning the dynamics of residue cover during fallow is available for this area. We report here results on the evolution of barley residues during two fallow periods under conventional tillage (CT), reduced tillage (RT) and no-tillage (NT). The three tillage treatments were compared under both continuous cropping (CC) and cereal–fallow (CF) rotation. The CC system involves a summer fallow period of 5–6 months and the CF rotation a long-fallow of 17–18 months. Effects of specific tillage operations on soil cover are also presented and discussed in relation to wind erosion control during the long-fallow period. Average dry mass of barley residues at harvest was 1395 and 729 kg ha −1 in the first and second year of the study, respectively. In general, crop residues at harvest were not significantly affected by tillage or cropping system. Primary tillage operations had the major influence on residue incorporation with reduction percentages of residue cover of 90–100% in CT (mouldboard ploughing) and 50–70% in RT (chiselling). During the two long-fallow periods, large clods (4–10 cm diameter) produced by mouldboard ploughing did not fully compensate for the complete burial of residues and the soil surface was insufficiently protected against wind erosion (soil covers <3% and random roughness ≈4%). The most critical period corresponded to that elapsed between primary and secondary tillage operations. The lack of residue-disturbing operations in NT makes this practice the best strategy for fallow management. After 17–18 months of fallow, the NT plots still conserved a surface residue cover of 10–15%. Similarly, standing residues, representing between 20 and 50% of the total residue mass, were also present on the no-tilled surface during the first 11–12 months of fallow. In general, RT plots maintained a soil erodibility condition similar to that of NT due to the combined effect of soil cover by clods and residues retained after tillage (5–15%) and the roughness created by clods (6–13%).

Effect of Cercospora zeae‐maydis infested maize residue on progress and spread of grey leaf spot of maize in central Uganda

SummaryThe spread of grey leaf spot caused by Cercospora zeae‐maydis from infested maize residue on the soil surface and progress over time were studied under tropical conditions at two locations in central Uganda, Kabanyolo and Namulonge, using a susceptible local cultivar, LP16. Infested maize residue collected the previous season was used as the inoculum source in varying amounts; 80% coverage, 40% coverage and 0% soil coverage were used to simulate no tillage, minimum tillage and maximum tillage with complete burial of residues. In all the seasons, disease spread was adequately described by a power law model, whereas disease progress over time was equally well represented by both Gompertz and logistic models. The time factor was highly significant (P &lt; 0.05) for disease development, indicating both increases in disease intensity over time and change in gradients with time. The amount of infested residue on the soil surface in the maize planting was highly significant (P &lt; 0.05) for slope (b) and intercept (a) of the linearised disease gradient. The gradient parameter (b) based on the average for the four directions from the residue source ranged from −0.96 to −0.08 in the second cropping season of 1999, from −2.16 to −0.01 and from −0.87 to −0.03 in the first and second seasons of 2000, respectively. The distance from the infested residue significantly affected foliar disease, but the direction from the residue inoculum source did not, nor was the distance by direction interaction significant. However, interactions between amount of residue and distance were significant. Percentage leaf area affected by grey leaf spot, the areas under disease progress curves and disease intercepts decreased with distance at both locations, but rate of disease increase (r) was generally constant with distance from residue source at Kabanyolo, but not at Namulonge. The relationship between disease severity and amount of residue cover appeared to be affected by the level of background inoculum. At Kabanyolo, where little background inoculum was present, differences were detected in disease severity parameters between the no‐residue plots and residue plots, whereas at Namulonge, where high background levels existed, there was no effect of residue on disease.

Tillage systems and soil ecology

Tillage systems affect the soil physical and chemical environment in which soil organisms live, thereby affecting soil organisms. Tillage practices change soil water content, temperature, aeration, and the degree of mixing of crop residues within the soil matrix. These changes in the physical environment and the food supply of the organisms affect different groups of organisms in different ways. One of the challenges of research in soil ecology is to understand the impacts of management on the complex interactions of all organisms at the soil community level. In addition to the response of organisms to soil manipulations, agriculturalists are interested in the actions of soil organisms on the physical and chemical environment in the soil. Soil organisms perform important functions in soil, including structure improvement, nutrient cycling, and organic matter decomposition. This paper discusses the effects of tillage practices on soil organism populations, functions, and interactions. Although there is a wide range of responses among different species, most organism groups have greater abundance or biomass in no-till than in conventional tillage systems. Larger organisms in general appear to be more sensitive to tillage operations than smaller organisms, due to the physical disruption of the soil, burial of crop residue, and the change in soil water and temperature resulting from residue incorporation. Variations in responses found in different studies reflect different magnitudes of tillage disruption and residue burial, timing of the tillage operations, timing of the measurements, and different soil, crop, and climate combinations. The paper concludes with a discussion of challenges for tillage researchers.

Folding of a pressure-denatured model protein.

The noncovalent complex formed by the association of two fragments of chymotrypsin inhibitor-2 is reversibly denatured by pressure in the absence of chemical denaturants. On pressure release, the complex returned to its original conformation through a biphasic reaction, with first-order rate constants of 0.012 and 0.002 s-1, respectively. The slowest phase arises from an interconversion of the pressure-denatured state, as revealed by double pressure-jump experiments. Below 5 microM, the process was concentration dependent with a second-order rate constant of 1,700 s-1 M-1. Fragment association at atmospheric pressure showed a similar break in the order of the reaction above 5 microM, but both first- and second-order folding/association rates are 2.5 times faster than those for the refolding of the pressure-denatured state. Although the folding rates of the intact protein and the association of the fragments displayed nonlinear Eyring behavior for the temperature dependence, refolding of the pressure-denatured complex showed a linear response. The negligible heat capacity of activation reflects a balance of minimal change in the burial of residues from the pressure-denatured state to the transition state. If we add the higher energy barrier in the refolding of the pressure-denatured state, the rate differences must lie in the structure of this state, which has to undergo a structural rearrangement. This clearly differs from the conformational flexibility of the isolated fragments or the largely unfolded denatured state of the intact protein in acid and provides insight into denatured states of proteins under folding conditions.

Development of Pleospora allii on garlic debris infected by Stemphylium vesicarium

Pseudothecia of Pleospora allii developed best on garlic leaf debris infected by Stemphylium vesicarium incubated at low temperature (5–10°C) and relative humidity (RH) close to saturation. RH of less than 96% prevented the formation of pseudothecia, while an incubation temperature of 15–20°C led to the early degeneration of pseudothecia. Under natural conditions, colonization by pseudothecia of unburied garlic leaf debris varied between seasons from 6.0 to 15.5 pseudothecia/mm2, whereas lower colonization levels were recorded when samples were buried. Pseudothecial maturity was reached 1–4 mo after the deposition of garlic debris on the soil surface and 15 days after the burial of residues. In the later case, pseudothecia degenerated with degradation of the plant debris. Ascospore release, which required rainfall or dew periods, occurred between late January and late April depending upon the year. A high correlation was found between pseudothecia maturation and four meteorological variables. Two of which, i.e. the number of hours with RH≥98% and with a mean temperature of 4.5–10.5°C, and the accumulated rainfall, explained most variability (adjusted R2=0.82−0.98 depending upon the year). A multiple regression equation relating the pseudothecia maturity index with these two variables could be used to forecast the epidemic onset of Stemphylium leaf spots in Southern Spain. Temporal progress of pseudothecia maturation was best fitted by a monomolecular model.

Use of a potential of mean force to analyze free energy contributions in protein folding.

A method for calculation of the free energy of residues as a function of residue burial is proposed. The method is based on the potential of mean force, with a reaction coordinate expressed by residue burial. Residue burials are calculated from high-resolution protein structures. The largest individual contributions to the free energy of a residue are found to be due to the hydrophobic interactions of the nonpolar atoms, interactions of the main chain polar atoms, and interactions of the charged groups of residues Arg and Lys. The contribution to the free energy of folding due to the uncharged side chain polar atoms is small. The contribution to the free energy of folding due to the main chain polar atoms is favorable for partially buried residues and less favorable or unfavorable for fully buried residues. Comparison of the accessible surface areas of proteins and model spheres shows that proteins deviate considerably from a spherical shape and that the deviations increase with the size of a protein. The implications of these results for protein folding are also discussed.

Dilemma of Industrial Wastewater Treatment: ABSTRACT

Today industry is being forced to meet quality standards in all water effluents discharged or proposed to be discharged to public waters. This national policy demands the removal of substances from water or management of the processing so that restricted materials do not reach the water environment. Generally these restricted materials have no value in their present form or place and are, therefore, wastes. Now the dilemma is this: having removed or isolated these materials at great cost, what do you do with them? Concentration of the materials may lessen cost of transportation and storage, but does not solve the ultimate disposal problem. There are millions of tons of industrial residues being stored in open pits above ground. Carbonates, hydrates, silicates, sulfates, oils, tars, acids, and brines can be found stored in diked areas near industrial centers. Some of these stored materials contain small quantities of toxic substances. All of these materials are subject to leaching and reentering the environment. Maintenance of these open pits to avoid pollution is a never-ending concern. The alternatives to pit storage have been ocean disposal, deep-well disposal, disposal by dilution during flood periods, and in the case of organic materials, incineration. One by one these alternatives are being legislated or regulated out of existence. The utopian philosophy of complete recycle is gaining popularity. The atomic energy industry has for years isolated dangerous materials, immobilized them, and buried them on reservations far removed from processing sites. Treatment of the water may cost as much as $1.00/gal. Transportation and burial of residues are a large added cost. Processing industries generate some very complicated wastewaters. The most difficult are those which contain both organic and inorganic substances in true solution. The dilemma is cause for national concern, requiring study and resolution. The road to complete recycling, if there is such a thing, is long and costly. Politicians must be forced to look at both sides of the environmental protection coin. End_of_Article - Last_Page 2089------------