Abstracts of Recent Publications


Barak, P, and S. Kruse. 2017. ADPF: Use Least Squares Polynomial Regression and Statistical Testing to Improve Savitzky-Golay. R package version 3.4.1. Available at CRAN (Comprehensive R Archive Network) under GPL-3 license, https://cran.r-project.org/package=ADPF.

This function takes a vector or matrix of data and smooths the data with an improved Savitzky Golay transform. The Savitzky-Golay method for data smoothing and differentiation calculates convolution weights using Gram polynomials that exactly reproduce the results of least-squares polynomial regression. Use of the Savitzky-Golay method requires specification of both filter length and polynomial degree to calculate convolution weights. For maximum smoothing of statistical noise in data, polynomials with low degrees are desirable, while a high polynomial degree is necessary for accurate reproduction of peaks in the data. Extension of the least-squares regression formalism with statistical testing of additional terms of polynomial degree to a heuristically chosen minimum for each data window leads to an adaptive-degree polynomial filter (ADPF). Based on noise reduction for data that consist of pure noise and on signal reproduction for data that is purely signal, ADPF performed nearly as well as the optimally chosen fixed-degree Savitzky-Golay filter and outperformed sub-optimally chosen Savitzky-Golay filters. For synthetic data consisting of noise and signal, ADPF outperformed both optimally chosen and sub-optimally chosen fixed-degree Savitzky-Golay filters. See Barak, P. (1995) <doi:10.1021/ac00113a006> for more information.

Obear, GR, P Barak, and DJ Soldat. 2016. Soil inorganic carbon accumulation in sand putting green soils II: Acid–base relationships as affected by water chemistry and nitrogen source. Crop Sci 56:1-11. doi: 10.2135/cropsci2015.06.0342

There is a widely held belief in the turfgrass industry that bicarbonate from irrigation water can accumulate and cause physical problems in the soil despite a lack of evidence for this claim. The objective of this study was to quantify accumulation of carbonate (soil inorganic C [SIC]) from irrigation water in a simulated root zone of a sand putting green fertilized with two different N sources (ammonium sulfate or potassium nitrate). To track SIC additions from irrigation water, sand columns were irrigated with low salinity, carbonate-enriched water containing 13C-labeled bicarbonate and compared with a control irrigated with deionized water. After 20 mo, which was equivalent to about 3.5 yr of typical irrigation on a golf course, soil pH, SIC, and δ13C were measured by depth. Acidity from nitrification of ammonium sulfate applications offset alkalinity inputs from carbonate-enriched irrigation water and resulted in net acidification of soils, especially from 0 to 5 cm in depth. Soil inorganic C accumulation was observed in columns irrigated with carbonate-enriched water but did not result in decreased air permeability of the root zone. There were no significant differences in soil δ13C among experimental treatments despite δ13C differences in turf leaf tissue. This suggests that SIC applied through irrigation may accumulate in the soil, but is subject to isotopic exchange with atmospheric CO2 (gas). These findings do not support the claim that irrigating turfgrass with water containing elevated levels of bicarbonate will negatively impact soil physical properties.

Barak, P. 2015. Electrodialysis stacks, systems, and methods for recovering ammonia and monovalent salts from anaerobic digestate. US Patent Application 20150308001. Publication date: Oct 29, 2015

Electrodialysis stacks comprising a series of electrodialysis cells and anaerobic digestion systems incorporating the electrodialysis stacks are provided. Also provided are methods of using the electrodialysis stacks and systems to recover nitrogen, in the form of ammonia, from separated anaerobic digestate. The electrodialysis stacks use monovalent-selective cation exchange membranes to concentrate ammonium ions and other monovalent ions in a concentrate stream, while discriminating against multivalent cations, which, as a result, are retained in a diluate stream. The electrodialysis stacks may use monovalent-selective anion exchange membranes to discriminate against multivalent anions, which, as a result, are selectively retained in a diluate stream.

Rosanoff, A, E Capron, P Barak, B Mathews and F Nielsen. 2015. Edible plant tissue and soil calcium:magnesium ratios: Data too sparse to assess implications for human health. Crop & Pasture Sci 66:1265–1277.http://dx.doi.org/10.1071/CP15085

Unlike yield, the plant calcium (Ca):magnesium (Mg) ratio increases at higher soil Ca:Mg and decreases at lower soil Ca:Mg. Edible plant tissue Ca:Mg at various soil ratios has not been robustly studied. Such studies are appropriate because high Ca:Mg dietary ratios may be associated with increased risk of chronic diseases such as cardiovascular disease and diabetes, and human dietary Ca:Mg ratio is rising as populations integrate more processed foods into traditional diets. This review explores whether increasing the soil Ca:Mg ratio is likely to increase edible plant tissue Ca:Mg ratio, a result that could, if substantial, affect human health. A literature search gathered published articles reporting Ca and Mg values for plants grown in soils or nutrient solutions with various Ca:Mg ratios. For each study, soil or solution ratio was plotted against plant ratio, and Pearson’s r and 2-tailed P values were calculated. Findings reveal that reporting Ca and Mg content of edible plant tissues is rare in studies assessing the impact of soil Ca:Mg on crop yields, nutrient uptake or crop quality; Ca:Mg of whole plants and most shoots increases as soil Ca:Mg rises; leaf Ca:Mg of some but not all crops increases as soil Ca:Mg rises; Ca:Mg ratios of edible grain, fruit and root tissues are smaller than those of leaves or shoots of the same crop; and Ca:Mg of grain, bean and fruit tissue may not respond to changes in soil Ca:Mg as much as Ca:Mg of plants, shoots and leaves. However, the data are too sparse for conclusions or even speculation. Further measurements of Ca and Mg in edible tissues destined for human consumption are necessary to asses any impact of soil Ca:Mg on the rising dietary Ca:Mg of humans and its health consequences.

Melby, ES, DJ Soldat, and P Barak. 2013. Preferential soil sorption of oxygen-18 labeled phosphate. Commun Soil Sci Plant Anal 44:2371-2377. doi: http://dx.doi.org/10.1080/00103624.2013.800100.

There is an increasing demand to develop a means to trace phosphorus (P) movement through the environment as excessive inputs of P have led to the eutrophication of many fresh water bodies. Oxygen-18 labeled phosphate (OLP) and natural abundance 18O have been used as tools for elucidating the dynamics of phosphorus in soils, yet much remains poorly understood. The objective of this research was to determine the extent of preferential soil sorption across the range of species contained within OLP. To accomplish this objective, a variety of soils were shaken with water containing 65.5 mg L-1 OLP-P for a 24 h period. Following shaking, the OLP species remaining in the solution were determined. Increasing the number of oxygen-18 atoms contained within the phosphate molecule by one resulted in a 1.8% increase in the amount of that OLP species sorbed to the soil surface, and this increase in sorption was uniform for all soils tested. Among the soil types, a strong correlation (r2 = 0.94) was found between the amount of phosphate sorbed and the Mehlich-3 phosphorus saturation ratio. These results will be useful for studies involving the use of natural abundance and enriched 18O-phosphate in soils and sediments.

Melby, E.S., D.J. Soldat, and P. Barak. 2013. Biological decay of 18O-labeled phosphate in soils. Soil Biol Biochem 63:124-128. doi: 10.1016/j.soilbio.2013.03.020.

There is an increasing demand to develop a means to trace phosphorus (P) movement through the environment as excessive inputs of P have led to the eutrophication of many fresh water bodies. 18O labeled phosphate has been suggested as a potential tool for tracing P, and other researchers are using information from natural abundance 18O levels of phosphate to study phosphorus cycling. The objective of this research was to determine the rate of biological de-labeling of 18O in soils. This objective was achieved using a laboratory incubation study in which three silt-loam textured soils were incubated with 250 mg kg-1 P18O4-P for a period of 3, 10, 30, or 50 d. The incubations were conducted on both sterilized and unsterilized soils. Following incubation, phosphate from soils was extracted with a modified Bray extractant and analyzed using electrospray ionization mass spectrometry to determine the distribution of labeled phosphate species. The half-life of P18O4 in the non-sterile soils ranged from 15 to 22 d, while there was no observed P18O4 de-labeling in sterile soils after 50 d. A parameterized numerical model was developed which provided insight into the dynamics of the individual labeled phosphate species, including their half-lives and relative concentrations across the incubation period. The use of P18O4 may be useful in areas where use of radioisotopes of P is restricted, and P18O4 has potential to be useful to elucidate the dynamics of the P cycle in soils.

Melby,E.S., D.J. Soldat, and P. Barak. 2011. Synthesis and detection of oxygen-18 labeled phosphate. PLoS ONE 6(4): e18420. doi:10.1371/journal.pone.0018420.

Phosphorus has only one stable isotope and therefore tracking P dynamics in ecosystems and inferring sources of P loading to water bodies have been difficult. Researchers have recently employed the natural abundance of the ratio of 18O/16O of phosphate to elucidate P dynamics. In addition, phosphate highly enriched in oxygen-18 also has potential to be an effective tool for tracking specific sources of P in the environment, but has so far been used sparingly, possibly due to unavailability of oxygen-18 labeled phosphate (OLP), and uncertainty in synthesis and detection. One objective of this research was to develop a simple procedure to synthesize highly enriched OLP. Synthesized OLP is made up of a collection of species that contain between zero and four oxygen-18 atoms, and as a result the second objective of this research was to develop a method to detect and quantify each OLP species. OLP was synthesized by reacting either PCl5 or POCl3 with water enriched with 97 atom % oxygen-18 in ambient atmosphere under a fume hood. Unlike previous reports, we observed no loss of oxygen-18 enrichment during synthesis in ambient atmosphere. Electrospray ionization mass spectrometer (ESI-MS) analysis was used to detect and quantify each species present in OLP. From this analysis it was determined that OLP synthesized from POCl3 contained 1.2% P18O16O3, 18.2% P18O216O2, 67.7% P18O316O, and 12.9% P18O4, and OLP synthesized from PCl5 contained 0.7% P16O4, 9.3% P18O316O, and 90.0% P18O4. We found that OLP can be synthesized using a simple procedure in ambient atmosphere without the loss of oxygen-18 enrichment, and ESI-MS is an effective tool to detect and quantify OLP that sheds light on the dynamics of synthesis in ways that standard detection methods cannot.

Avila-Segura, M, P. Barak, J. Hedtcke and J.L. Posner. 2011. Nutrient and alkalinity removal by corn grain, stover and cob harvest in Upper Midwest USA. Biomass and Bioenergy 35:1190-1195.

In the USA, most corn stover currently remains in fields as crop residue that provides soil erosion control and maintains soil organic carbon levels. This stover is a potential biofuel feedstock for direct combustion, pyrolysis, and ethanol fermentation. At a research site in south central Wisconsin, the northern edge of the US Corn Belt, corn grain harvest averaged 9.8 Mg ha 1 DM over a 6-year period, 1997 to 2002. Removal of all stover could recover an additional 7.2 Mg ha–1 y–1 DM and, in the process, remove an additional 47, 6, 81 and 197 kg ha–1 y–1 of N, P, K and calcium carbonate equivalent, respectively. The fertilizer replacement cost for stover removal is 32 $ Mg–1 DM, which is 95% of the fertilizer value of the grain. However, most of the N, P, K and alkalinity of the stover is found in the leaves, stalk, and husks, not in the cob. At our study site, complete stover removal would export 235 $ ha–1 y–1 of fertilizer and limestone, mainly as K, while cob export would be worth 20 $ ha–1 y–1 in nutrient equivalents. Based on this research, removal of cobs only is equivalent to 16.6% of total stover removal but with a greatly reduced fertilizer replacement cost of 17 $ Mg–1 DM and the same energy density.

Soldat, D.J., P. Barak, and B.J. Lepore. 2009. Microscale colorimetric analysis using a desktop scanner and automated digital image analysis. J. Chem. Educ.86:617-620 (plus 6 pp. supplemental online material and AnalyzeMicroplateStatistics ImageJ macro)

In recent decades, several standard colorimetric reactions for chemical analysis have been miniaturized to microwells on microplates, including many of those methods useful for environmental measurements. Advantages of method miniaturization include a reduction in reagents required, improved safety, reduced waste stream, and increased sample throughput. However, the widespread use of microscale techniques employing microplates in classroom settings is likely limited by the high cost of microplate readers. Although spectrophotometers read peaks of specific wavelengths, absorbance spectra tend to be relatively broad and measurements at specific wavelengths are highly autocorrelated with those of nearby neighbors, which implies that broadband intensity data of red, green and blue channels may indeed be adequate for digital colorimetric quantification. In this manuscript, we demonstrate that digital image analysis of a scanned microplate image can substitute for a spectrophotometer for several common quantitative microscale procedures. This finding allows for cost effective and microscale quantification of several compounds to be demonstrated in the laboratory. Additionally, popular teaching and learning activities such as water quality monitoring can now be performed accurately and inexpensively using digital image analysis.

Lepore, B.J., and P. Barak. 2009. A colorimetric microwell method for determining bromide concentrations. Soil Sci Soc. Am. J.73:1130-1136; doi:10.2136/sssaj2007.0226.

Bromide (Br-) is commonly used as a tracer in studies of water and chemical transport in soil and rock because it is relatively nonreactive with soil and rock constituents and because of its low environmental background concentrations. Based upon a largely ignored modification of an APHA standard colorimetric method for determining Br- using phenol red and chloramine-T (Jones, D.R. 1993. Improved spectrophotometric method for the determination of low levels of bromide. Anal. Chim. Acta 271:315-323), we correct an internal error and recast the technique for use with 96-well microplates. Furthermore, the addition of thiosulfate to quench the undesirable chlorination reaction as previously published is shown to be unnecessary and even detrimental following the use of ammonium to produce chloramine from excess chlorine species. The method detection limit is 0.11 mg L-1 Br-; negative interference with dissolved organic carbon can be addressed by either standard additions or solid phase extraction with C18 sorbent. By reducing sample size from 300 to 20 ìL and concentrations of phenol red and chloramine-T, the concentration range can be expanded from 12 mg L-1 Br- to much as 300 mg L-1 Br-.

Barak, P., M.E. Tabanpour, M. Avila-Segura, J.M. Meyer. 2007. Struvite Crystallization. 28pp. US Patent No. 7,182,872; rights assigned to WARF. [pdf]

The present invention provides a method and apparatus for removing phosphorus from phosphorus containing waste. In one embodiment, the method is preferably carried out by contacting the phosphorus containing waste with a noncellular membrane and precipitating phosphorus from the waste as struvite. Another aspect of the invention includes a method of removing phosphorus from phosphorus containing sewage comprising filtrates and biosolids. The removal of phosphorus as struvite occurs in two stages as primary and secondary removal. In the primary removal process, the sewage from a dewatering unit is contacted with a first polymeric membrane reactor and the phosphorus is removed as primary struvite. Subsequently Mg is added so as promote struvite formation and the secondary removal process of struvite. In the secondary removal process, the sewage from GBT Filtrate well or Centrifuge Liquor well is contacted with a second monomolecular membrane and the phosphorus is removed as secondary struvite.

Barak, P., and E.A. Nater. 2005. The Virtual Museum of Minerals and Molecules: Molecular visualization in a virtual hands-on museum. J. Nat. Resour. Life Sci. Educ. 34:67-71.

The Virtual Museum of Minerals and Molecules (VMMM) is a web-based resource presenting interactive, 3-D, research-grade molecular models of more than 150 minerals and molecules of interest to chemical, earth, plant, and environmental sciences. User interactivity with the 3-D display allows models to be rotated, zoomed, and specific regions of interest to be highlighted. The VMMM has been online since 1998 and currently serves 100 000 to 250 000 unique visitors annually from two mirror sites. In concept, it is a blend of a static bricks-and-mortar physical museum with wings, galleries, and displays with dynamic 3-D first-person video games. This museum is virtual not only in the sense that it exists in electronic format but also because the molecular size of the objects makes them colorless and imperceptibly small. To date, molecular visualization has been enabled in browsers using a proprietary third-party plug-in; compatibility with diverse platforms and browsers has been reduced over past years and recourse to open-source, molecular visualization Java applets may be required to avoid technological obsolescence.

Avila-Segura, M., J.W. Lyne, J.M. Meyer, and P. Barak. 2004. Rapid spectrophotometric analysis of soil phosphorus with a microplate reader. Comm. Soil Sci. Pl. Anal. 35:547–557.

The demands of environmental P research require that laboratories process a large amount of samples accurately and efficiently. The application of tools common to molecular biology is evaluated for their practical use in expediting the measurement of Bray P, total P, and P sorption isotherms using microcentrifuges, precision multichannel pipetters, microplates, and microplate readers (multi-sample colorimeters). Our results show that the methods introduced here provided reliable data with error ranges comparable to similar wet chemistry analyses. The micro-scale techniques allow the laboratory processing of thousands of Bray P, total P by standard additions and P sorption curves efficiently and accurately and therefore provide a suitable alternative to the conventional macro-scale batch sizes for these standard soil P tests.

Grunwald, S., and P. Barak. 2003. 3D geographic reconstruction and visualization techniques applied to land resource management. Trans. GIS 7(2):231-241.

Optimized land resource management depends on reliable and detailed information describing the spatial distribution of soils, geology, topography, and land use. Soil-landscapes are three-dimensional (3D) systems commonly represented using 2D maps utilizing geographic information systems. To address 3D soil-landscape reality is crucial for land resource management in terms of crop growth and transport processes (e.g. nitrate leaching) that are driving soil and water quality. Our objective was to investigate the usefulness of 3D geographic information technology (GIT) applied to land resource management. Our approach is based on 2D and 3D ordinary kriging interpolating surface and subsurface attributes to reconstruct soil-landscapes. We used Virtual Reality Modeling Language, which is a web-based 3D graphics language, to visualize objects (e.g. voxels, polyhedrons) representing soil and land-scape attributes. We produced a 3D block model showing the spatial distribution of bulk densities and relief for a site in southern Wisconsin and a 3D stratigraphic model showing the spatial distribution of soil horizons and relief for a site in northern Florida. Emerging GIT was used to develop 3D soil-landscape models describing continuous changes of soil and landscape attributes. Combining multimedia elements (e.g. WWW, 3D visualization, and interactivity) can produce insight that would not arise from using of the elements alone. Three-dimensional scientiÞc visualization is a powerful tool to help us see what is invisible from above the ground.

Grunwald, S., and P. Barak. 2002. The use of VRML for virtual soil landscape modeling. System Analysis Modelling Simulation (SAMS) 41:755-776.

The utilization of three-dimensional (3-D) graphical design and scientific visualization of the soil landscape continuum is still in its infancy. The objective of this study was to investigate the use of Virtual Reality Modeling Language (VRML) to create virtual 3-D soil landscape models representing natural soil landscape components. Virtual Reality Modeling Language is an object-oriented, 3-D graphics language suitable for stand-alone or browser-based interactive viewing. Our virtual soil landscape models showed the spatial distribution of soil patterns and terrain characteristics. We were able to integrate features from geographic information systems, such as storage and minipulation, with features from scientific visualization, such as 3-D graphical design, animation of objects, interactivity and accessibility via the world wide web.

Grunwald S., P. Barak, and D.J. Rooney. 2001. Web-based virtual models for the earth science community. ASAE International Meeting in Sacramento, CA, July 29-August 1, 2001; Paper No. 013029.

Optimized agricultural management depends on reliable and detailed information describing the spatial distribution of soils, geology (parent material), and topography. Subsurface attributes (earth data) have in common that they vary through three-dimensional (3-D) space and through time. Our goal was to overcome current limitations of geographic information systems to manage, analyze, and visualize geographic data in two dimensions (2-D). In this paper we present an approach to reconstruct and visualize soil-landscapes with focus on web-based dissemination of model output. Our approach is multi-dimensional, multi-variate, spatially object-oriented, transferable, scalable, and expandable. We used geo-referenced subsurface and topographic attributes from several sites in southern Wisconsin and northwestern Ohio to demonstrate the capabilities of our approach. Reconstruction was based on 2-D and 3-D ordinary kriging utilizing Environmental Visualization System (EVS) software and implemented in Virtual Reality Modeling Language (VRML). Three different types of soil-landscape models were distinguished: (i) Models representing subsurface attributes as points (ii) Models representing subsurface objects as polyhedrons or “volume models” and (iii) Block models consisting of voxels (volume cells). A server hosts the virtual soil-landscape models, which are accessible by multi-clients via an interface coded in HTML. These models are interactive, platform independent and enable users to analyze, explore and gain insight into the spatial distribution of topographic and subsurface attributes in 3-D geographic space. Numerous agricultural tasks are supported using our approach including 3-D soil surveys, informed decision-making, assessment of environmental quality, farm management, land use planning, and many more. Virtual soil-landscape models are beneficial in disseminating geo-referenced earth data to educators, researchers, government agencies, and the general public.

Orvis, KS, IL Goldman, and P. Barak. 2001. Excess sulfate supply and onion-induced human antiplatelet activity. J. Plant Nutr. Soil Sci. 164:457-462.

Awareness is growing of health-promoting functional foods and the use of various plants as nutraceuticals. Due to a suite of organosulfur compounds, onion, and other vegetable Alliums possess a unique antiplatelet effect that may promote cardiovascular health because aggregating platelets can lead to heart attack and stroke. Investigation of the consequences of S nutrition in onion has primarily focused on levels of S ranging from deficiency to just above sufficiency; however, little work has been conducted to examine the effects of supraoptimal S nutrition on organosulfur-based traits. Four onion selections were grown in hydroponic solutions with 2, 7, and 12 mM SO42- -S in greenhouse experiments during 1995-1996 and 1996-1997. Onion plants were separated into root, leaf, and bulb portions and analyzed for mineral content. Onion bulb extracts were assayed for in vitro human antiplatelet activity. Bulb and leaf S were not affected by increasing solution culture S, but root S was increased by 98 % when solution culture S was increased from 2 mM to 12 mM. Similar increases in root Ca and Al were detected, suggesting CaSO4 and AlSO4+ were accumulated in and on the root. No directional change in antiplatelet activity was detected as S was increased from 2 to 12 mM. This lack of significant change in antiplatelet activity with increasing S levels suggests that modification of this trait by simply increasing S levels may not be feasible in a solution culture environment.

Grunwald, S., and P. Barak. 2001. Virtual Reality modeling in earth sciences. p. 216-221. In: C. Landauer and K.L. Bellman. (ed.) The Proceedings of the International Conference on Simulation and Multimedia in Engineering Education & Virtual Worlds and Simulation. Soc. Modeling and Simulation International, San Diego, CA. [ISBN:1-56555-224-5; Western MultiConference on Computer Simulation. Phoenix, AZ, 7-11 Jan 2001] (illustrations at http://www.soils.wisc.edu/~barak/wmc2001/).

Introduction: The earth sciences commonly face difficulties in scientific visualization due to widely varying scales, multiple character attributes, multiple layering, and three- and four-dimensional reality. For example, earth science data at the landscape scale, traditionally stored on two-dimensional paper maps, have been transformed during the last two decades into digital format using geographic information systems (GIS), which is still an on-going process. Even so, state-of-the-art GIS incluse the lack of three dimensional (3-D) and four-dimensional (4-D) data handling and visualization due to software limitations. Similar issues limit display of the structure and function at micro-scale of the molecules and crystalline minerals that constitute earth materials. recently, earth scientists entered the realm of virtual reality (VR) to make use of innovative techniques developed for scientific visualization. Desktop VR models are implemented using....

Sherman, L.A., and P. Barak. 2000. The solubility and dissolution kinetics of dolomite [CaMg(CO3)2] in Ca-Mg-HCO3/CO3 solutions at 25°C and 0.1 MPa carbon dioxide. Soil Sci. Soc. Am. J. 64:1959-1968.

Dolomite solubility in water has been measured by a number of different methods over the past several decades, yielding inconsistent and unreliable results that vary over three orders of magnitude. The most commonly used "best value" for dolomite solubility in water is based on HCl solution calorimetry at 300.15 K, which is not confirmed by earlier determinations based on heat capacity of dolomite nor by more recent acid solution and metal oxide melt calorimetric measurements. In this study, the solubility of a high purity dolomite was measured directly by monitoring dissolution in Ca Mg HCO3/CO3 solutions designed to bracket the presumed solubility product of dolomite, pKs dolomite [= log (Ca2+)(Mg2+)(CO32-)2 ; where ( ) are activities at equilibrium], between 16.0 and 19.0, at 1 atm CO2 and 25 C. The use of gas-permeable, water-impermeable membranes over the dissolution vessels allowed for maintenance of an open system for CO2, with minimal water loss over the course of the 672-day experimental period. The dolomite dissolved congruently in Ca Mg HCO3/CO3 solutions with initial ion activity products [pIAPdolomite = log (Ca2+)(Mg2+)(CO32- )2; where ( ) are measured activities] greater than 17.5. Both calcite and magnesian calcites can be ruled out as controlling solubility in these measurements. Based on statistical inference by comparison of alkalinity in unseeded (control) and dolomite-seeded solutions, the pKs dolomite is between 17.4 and 17.0, expressed as 17.2 ± 0.2. A previously proposed kinetic model of successive reactions for dolomite dissolution near equilibrium–a fairly rapid dissolution of the CaCO3 component in equilibrium and a rate-limiting protonation reaction dependent upon the activity of the MgCO3 component–appears to fit the experimental data.

Grunwald, S., P. Barak, K. McSweeney, and B. Lowery. 2000. Soil landscape models at different scales portrayed in Virtual Reality Modeling Language (VRML). Soil Science 165:598-615 (illustrations at http://www.soils.wisc.edu/soils/3D_SL_models/3Dsoils.html)

Most state-of-the-art manipulation and visualization of soil data use geographic information systems to portray soil landscapes in two dimensions (2-D). Nevertheless, soil attributes are distributed continuously in three dimensions (3-D) across landscapes. The objective of this study was to investigate the use of Virtual Reality Modeling Language (VRML), a 3-D graphics language suitable for stand-alone or browser-based interactive viewing, to create 3-D soil landscape models at different scales. Four different locations in southern Wisconsin were selected to represent pedon, catena, catchment, and soil region scale. Soil data, including texture, cone index, and depth of soil layers, were used in conjunction with topographic attributes to create 3-D soil landscape models. Spatial modeling techniques comprised 2-D and 3-D ordinary kriging. We used Environmental Visualization Software (EVS) to export the geometry of 3-D objects, which were enhanced to include: (i) viewpoints, (ii) Munsell colors, (iii) texture maps, (iv) 3-D cross-section animation, (v) animations such as zooming, rotation, and (vi) primitive shapes to highlight areas of interest. Virtual reality modeling language is capable of describing and visualizing extremely complex shapes, such as complex soil layers or terrain. Visualization of Munsell soil colors was difficult to implement because there is no hardware and software independent color-management system available in VRML. Animation techniques were valuable to highlight specific characteristics of each model. The accessibility of interactive VRML models via the World Wide Web and the portability of these models across platforms facilitate soil science to enter the virtual world of cyberspace.

Mafongoya, P.L., P. Barak, J.D. Reed. 2000. Carbon, nitrogen and phosphorus mineralization of tree leaves and manure. Biol. Fert. Soils 30:298-305.

Farmers in developing countries cannot afford inorganic fertilizers. Multipurpose tree leaves or livestock manure are major sources of nutrients for soil fertility replenishment. Nutrient release from these organic inputs depends on their chemical composition and on soil properties. This study determined the chemical composition of leaves of four African browse species and manure from goats fed leaves as protein supplements, and their mineralization of C, N and P. Cumulative evolved CO2 was significantly correlated with the initial N content of the organic inputs (r 0.83, P<0.05) and the C:N ratio (r 0.80, P<0.05), and was negatively correlated with the lignin:N ratio (r -0.7, P<0.05). Cumulative P released was negatively correlated with the C:P ratio (r 0.76, P<0.05) and positively correlated with initial P content of the organic amendments (r 0.76, P<0.05). Cumulative N mineralized was not significantly correlated with initial N, Lignin or P concentrations of the organic inputs. Leaves from Acacia karro and Acacia nilotica had high concentrations of polyphenols, which may have caused immobilization of N in both leaves and manure. Gliricidia sepium leaves had low amounts of soluble polyphenols, a high N content and a high rate of N mineralization, but the manure from goats fed Gliricidia leaves immobilized N. The leaves of all browse species immobilized P, but the manure released P. The results suggested that some browse leaves cannot meet the N and P requirements of crops due to their low P content and prolonged N and P immobilization. However, the manures had higher P contents and rates of P mineralization, which suggested that manure is a good source of P for crops. The implications of these results for nutrient cycling in mixed farming systems is discussed.


Starr, G.C., P. Barak, B. Lowery, and M. Avila-Segura. 2000. Soil particle concentrations and size analysis using a dielectric method. Soil Sci. Soc. Am. J. 64:858-866.

Limitations of traditional methods for particle size analysis warrant the investigation of new techniques. An alternative method based on the difference between the dielectric constant of soil solids (~4) and dispersing solution (~81) was developed. We determined changes in suspended sediment concentrations (C) using a coaxial probe placed on the surface of a dispersed soil suspension by monitoring changes in the apparent dielectric constant over time following complete mixing. A single point calibration for each sample was obtained using the known initial concentration. A refractive index (n) model of the suspension dielectric properties gave the slope of a C vs. n equation for changes in silt size (0.002 to 0.05 mm) particles. A magnetic stirring rod was used to homogenize the dispersion and temperature changes were minimized given the rapid measurement time. Using the dielectric method, particle size distributions were measured on a 1- to 2-g sample with 400-s settling time because the effective depth of measurement was only 1.5 mm. Wet sieving was used to remove the sand fraction. Comparisons between the silt/clay fractions obtained using the dielectric and pipette methods were in agreement. The combination of speed, automation, small sample size, and nearly continuous data should be balanced against the higher cost of the equipment necessary for the dielectric method.


Barak, P., B.O. Jobe, A. Krueger, L.A. Peterson, and D.A. Laird. 1997. Effects of long-term soil acidification due to agricultural inputs in Wisconsin. Plant and Soil 197:61-69.

Agroecosystems are domesticated ecosystems intermediate between natural ecosystems and fabricated ecosystems, and occupy nearly one-third of the land areas of the earth. Chemical perturbations as a result of human activity are particularly likely in agroecosystems because of the intensity of that activity, which include nutrient inputs intended to supplement native nutrient pools and to support greater biomass production and removal. At a long-term fertility trial in South-Central Wisconsin, significant depletion of exchangeable Ca2+ and Mg2+, increases in exchangeable acidity, decline in CEC, and decline in base saturation have been noted in association with application of ammoniacal N fertilizer. Plant analysis shows that a considerable portion of the alkalinity generated by assimilation of N (and to a lesser extent by S) is sequestered in the above-ground plant parts as organic anions and is not returned to the soil if harvested. Elemental analysis of Ca-saturated soil clays indicates an irreversible loss of 16% of the CEC of the soil clay and minor increases in Fe and Al. The reversibility of these changes due to prolonged acidification is doubtful if the changes are due to soil weathering.


Hernández-Apaolaza, L., P. Barak, and J.J. Lucena. 1997. Chromatographic determination of commercial Fe(III)-chelates of EDTA, EDDHA and EDDHMA. J. Chromatogr. A 789:453-460.

The use of synthetic iron chelates is the most common and effective way to treat iron chlorosis in plants. Using an ion-pair HPLC method previously proposed by the authors, it was found that the older commercial products reached the percentage of Fe chelated indicated by the manufacturer, but in no case did the current products reach their nominal, or legal, composition. Moreover, the current products of FeEDDHA showed significant additional chromatographic peaks that, based on published synthesis pathways for these type of compounds, may correspond to para-para FeEDDHA or ortho-para FeEDDHA, sterically-hindered isomers of Fe-EDDHA that are of little or no value as an iron chelate for agricultural purposes.


Barak, P., and I.L. Goldman. 1997. Antagonistic relationship between selenate and sulfate uptake in onion (Allium cepa): implications for the production of organosulfur and organoselenium compounds in plants. J. Agric. Food Chem. 45:1290-1294.

The antagonistic relationship between sulfur and selenium accumulation in onion plants grown in solution culture with sulfate and selenate was investigated. In the absence of Se, plant S concentrations ranged from 0.6 to 1.45% at S solution culture levels of 0.8 mol m-3 (standard nutrient solution) and 14.8 mol m-3 SO4(gypsum saturated), respectively. Increasing levels from 1 to 8 g m-3 SeO4-Se did not increase Se content beyond 158 ± 19 mg plant-1, although plant concentrations ranged from 200 to over 1000 mg Se g-1 dry matter. At a constant Se level, increasing S in solution culture reduced plant dry matter Se concentration by 80%. When the antagonistic relationship between these two elements is expressed as a molar ratio, S/Se in plant dry matter is nearly identical to S/Se in solution culture. These data suggest S must be supplied at relatively low levels to produce high concentrations of plant Se.


Miglioranza, E., P. Barak, K. Kmiecik, and J. Nienhuis. 1997. Comparison of soil and genotypic effects on calcium content of snap bean pods. HortScience 32:68-70.

Humans need approximately 1200 mg of calcium (Ca2+) daily in adolescence to ensure maximal bone accretion and to potentially prevent osteoporosis later in life. A possible supplemental source of Ca2+ is snap bean pods, which are relatively high in calcium content compared to other vegetables. The objective of this experiment was to determine the influence of soil Ca2+ fertilization levels on the amount of Ca2+ in pods of different snap bean cultivars. The addition of gypsum (CaSO4.2H2O) to the soil did not affect the Ca2+ content of pods, even though Ca2+ in the soil solution increased from 4 mM to l5 mM. Calcium contents of pods of different snap bean genotypes range from 4.1 to 5.7 mg Ca2+ g-1 DW. The genotypes that had the highest Ca2+ content in the pods were 'Top Crop', 'Astrel', 'Tenderlake' and 'True Blue'. Pods from 'Labrador' and 'Roma II' had the lowest Ca2+ content. The results suggest that factors other than Ca2+ supply influenced the Ca2+ content of the snap bean pod. Therefore, increased Ca2+ content of pods may be better achieved through breeding and selection rather than Ca2+ fertilization when Ca2+ levels in soil are sufficient.


Liu, Y.-J., D.A. Laird, and P. Barak. 1997. Release and fixation of NH4 and K under long-term fertility management. Soil Sci. Soc. Am. J. 60:310-314.

Improved nutrient use efficiency in production agriculture is a research priority for both agronomic and environmental reasons. To achieve this goal, a thorough understanding is needed of both short-term and long-term nutrient dynamics in soils. The specific object of this study was to investigate the effect of long-term fertility management on the dynamics of fixed and exchangeable NH4 and K in a typical upper Midwestern agricultural soil. Soil samples (0-20 cm) were collected from long-term (30 yr) fertility plots near Arlington, WI. Fixed and exchangeable NH4 and K were determined for plots receiving 0 and 252 kg ha-1 K (from 1962-1982) and 0, 68, 112, 168 kg ha-1 N (from 1962-1982) as urea or NH4NO3. Levels of exchangeable NH4, fixed NH4, and fixed K were similar for all treatments. Exchangeable K was significantly higher in plots receiving 252 kg ha-1 K than those receiving no K. Levels of exchangeable K were also higher in plots receiving no N than in plots receiving N fertilizer. Fixation capacities for both NH4 and K were significantly reduced by sustained high rates of K fertilization, but not by N fertilization. These results suggest that levels of fixed NH4 can be neither built up nor depleted through long-term fertility management. On the other hand, levels of exchangeable K and both NH4 and K fixation capacities are influenced by long-term fertility management.


Barak, P., C.A. Seybold, and K. McSweeney. 1996. Self-similitude and fractal dimension of sand grains by computer-assisted image analysis. Soil Sci. Soc. Am. J. 60:72-76.

Fractal theory postulates that geological materials possess a noninteger, fractal dimension describing length/surface/volume relations and particle size distribution. We examined sand grains, composed largely of quartz, from several horizons of Wisconsin soils derived from glacial outwash for fractal dimension using image analysis of reflected light micrographs with NIH Image software.

No evidence was found to support other than a Euclidean, i.e., regular dimension, relating the geometric properties of: 1) measured particle perimeter as a function of magnification or 2) particle area and perimeter. In addition, particle size distributions were better fit by log normal distribution than by a fractal fragmentation dimension. Fractal theory would not appear to provide a useful description for these soil materials.


Barak, P., L.A. Sherman, and B.O. Jobe. 1996. Comments on "Design and construction of a personal-computer-based automatic titrator". Soil Sci. Soc. Am. J. 60:630.

As an alternative to a relatively complicated equipment configuration described by Kinniburgh et al. (1995; Soil Sci. Soc. Am. J. 59:417-422], a Metrohm Dosimat 665 automatic burette and an Orion pH/ISE meter No. 720A can be connected by serial cables to a personal computer programmed with QBasic or QuickBasic for research-grade pH-stat and custom titration routines. [--Authors' summary]


Barak, P., Smith, J.D., Krueger, A.R., and Peterson, L.A. 1996. Measurement of short-term nutrient uptake rates in cranberry by aeroponics. Plant, Cell, and Environ. 19:237-242.

Aeroponics, a soilless plant culture system in which fresh nutrient solutions are intermittently or continuously misted onto plant roots, is capable of sustaining plant growth for extended periods of time while maintaining a constantly refreshed nutrient solution. Although used relatively extensively in commercial installations and in root physiology research, use of aeroponics in nutrient studies is rare.

The object of this study was to examine whether nutrient uptake rates could be calculated for aeroponic systems by difference using measurements of concentrations and volumes of input and efflux solutions. Data were collected from an experiment with cranberry plants (Vaccinium macrocarpon Ait. cv. Stevens) cultured aeroponically with nutrient solutions containing various concentrations of ammonium-N and isotopically-labeled nitrate-N. Validation of the calculated uptake rates was sought by: 1) evaluating charge balance of the solutions and total ion uptake (including proton efflux), and 2) comparison with N-isotope measurements. Charge balance and proton efflux calculations required use of chemical modeling of the solutions to determine speciation of dissolved phosphate and acid neutralizing capacity (ANC).

Results show that charge balance requirements were acceptably satisfied for individual solution analyses and for total ion uptake when proton efflux was included. Relative rates of nitrate/ammonium uptake determined by difference were in agreement with those determined by isotopic techniques. Additional information was easily obtained from this experimental technique, including evidence of diurnal variation in nutrient uptake, correlation between ammonium uptake and proton efflux, and the relationship between ion concentration and uptake. Use of aeroponic systems for nondestructive measurement of water and ion uptake rates for numerous other species and nutrients appears promising.


Lucena, J.J., P. Barak, and L. Hernández-Apaolaza. 1996. Isocratic ion-pair high-performance liquid chromatographic method for the determination of various iron(III) chelates. J. Chromatogr. A.727:253-264.

The micronutrient iron, an essential element for plant growth, is usually added as fertilizer in chelated form. An isocratic ion-pair chromatographic method was developed to identify and determine the total amount of chelate in fertilizers. Iron(III) chelates containing ethylenediaminetetraacetic acid (EDTA), diethylenetriaminepentaacetic acid (DTPA), trans-1,2-cyclohexanediaminetetraacetic acid (CDTA), ethylenediamine(o-hydroxyphenylacetic) acid (EDDHA), also known as N,N'-ethylenebis-2-(o-hydroxyphenyl)glycine (EHPG), ethylenediamine(o-hydroxy-p-methylphenylacetic) acid (EDDHMA), N,N'-bis-(2-hydroxybenzyl)ethylenediamine-N,N'-dipropionic acid (HBED), and N,N'-bis-(2-hydroxybenzyl)ethylenediamine-N,N'-diacetic acid (HBEP) were well-separated by this method. The mobile phase contained 0.03 M tetrabutylammonium chloride and 30% acetonitrile at pH 6.0. The stationary phase was a LiChrospher RP=18 column, the injection volume 20 µL, and the flow rate 1.5 mL/min. For the iron(III)-EDDHA chelate, linear range studies showed that the method is capable of determining Fe concentration between 0.5 and 150 µg/mL, which permits the analysis of the concentrations found in commercial fertilizers. With this method, separation and identification of the iron(III) complexes were obtained with good resolution and selectivity, including the separation of the geometric isomers of the complexes, in 15 min.


Barak, P. 1995. Smoothing and differentiation by an adaptive-degree polynomial filter. Anal. Chem. 67:2758-2762.

The Savitzky-Golay method for data smoothing and differentiation calculates convolution weights using Gram polynomials that exactly reproduce the results of least-squares polynomial regression. Use of the Savitzky-Golay method requires specification of both filter length and polynomial degree to calculate convolution weights. For maximum smoothing of statistical noise in data, polynomials with low degrees are desirable, while high polynomial degree is necessary for accurate reproduction of peaks in the data.

Extension of the least-squares regression formalism with statistical testing of additional terms of polynomial degree to a heuristically-chosen minimum for each data window leads to an adaptive-degree polynomial filter (ADPF). Based on noise reduction for data that consist of pure noise and on signal reproduction for data that is purely signal, ADPF performed nearly as well as the optimally-chosen fixed-degree Savitzky-Golay filter and outperformed suboptimally-chosen Savitzky-Golay filters. For synthetic data consisting of noise and signal, ADPF outperformed both optimally-chosen and suboptimally-chosen fixed-degree Savitzky-Golay filters.

Now available at https://cran.r-project.org/package=ADPF. Code implementation is also available in Robert de Levie's 'How to Use Excel in Analytical Chemistry and in General Scientific Data Analysis' (Cambridge Univ. Press, 2001) and at http://www.cambridge.org/resources/0521642825/1253_73804.xls. Implementation is also available in MatLab format at the MatLab Central file exchange smoothing and differentiation

Errata: (a)(0)=0 should read (a)(0)=1


Barak, P., and P.A. Helmke. 1993. "The chemistry of zinc" pp. 1-13. in: A. Robson (ed.) Zinc in Soils and Plant. Proc., Internat. Symp. on "Zinc in Soils and Plants", Perth, Australia. Kluewer Acad. Press, Dordrecht.

Zinc is a metallic element with atomic number 30 and stable isotopes of mass 66, 67, 68, and 70, averaging 65.38 a.m.u. The terrestrial chemistry of Zn is that of Zn (II) rather than Zn(0). The Zn (II) ion has an electron configuration of ls2, 2s2, 2p6, 3d10, and therefore lacks unfilled d subshells in the well-known oxidation state, the requisite criterion for true transition metals. Zinc(II) has an ionic radius comparable with Mg(ll) but a Lewis acidity more like that of the smaller Cu(ll) ion.

Numerous zinc minerals-sulfides, sulfates, oxides, carbonates, phosphates, and silicates - have been described, most containing tetrahedral or octahedral coordination polyhedra with either apical S or O. Several minerals contain both tetrahedrally and octahedrally coordinated Zn(II), while others have fivefold coordination polyhedra alternating with octahedrally coordinated Zn(lI), reflecting the full and spherical 3d subshell which does not favour one coordination over another. The stabilities of aqueous zinc complexes have been measured for hydroxides, chloride, carbonate, sulfate, sulfide, phosphate, simple organic acids, amino acids, and synthetic chelates. Coordination of Zn(ll) in aqueous complexes is usually octahedral, although fourfold and fivefold coordination are also known.

Zinc is an essential element for terrestrial life since it is required as either a structural component or reaction site in numerous proteins, the zinc-binding portions of which are highly conserved among species. Zinc sites in proteins consist of Zn polyhedra with apical S, N, or O, associated with cysteine, histidine, glutamic acid, aspartic acid, and water. Coordination numbers for zinc range from four in the case of structural Zn associated with four thiol groups derived from cysteine to six in the case of a number of reactive sites containing O and N as apices.

The total concentration of zinc in soils depends on the composition of the parent material and soil mineralogy, especially the concentration of quartz, which tends to dilute most elements. Only a small fraction of the total zinc is exchangeable or soluble. About one-half of the dissolved zinc exists as the free hydrated cation. The concentration of dissolved complexes of zinc with inorganic ligands can be estimated by computer-implemented models and total concentrations as input. Similar approaches with organic ligands await further research. Most analytical determinations of zinc are made by spectrometric techniques such as atomic absorption spectrophotometry, inductively coupled plasma atomic emission spectroscopy, and inductively coupled plasma mass spectroscopy.


Welhouse, G., P. Barak, and W.F. Bleam. 1993. Dimerization constants of atrazine and CF3-labeled atrazine. J. Phys. Chem. 97:11583-11589.

A nonlinear optimization procedure is developed to find the dimerization constants of atrazine from the NMR chemical shifts of four of its NH protons. The NH protons identify four active sites which interact pairwise by cooperative association to form a total of 10 hydrogen-bonded dimers. Each active site is assumed to have a partial dimerization constant related to its chemical potential, and the partial constants are used to develop equations which fit the chemical shift data to a cooperative dimerization model. Partial dimerization constants are multiplied together pairwise to obtain the dimerization constant for each of the 10 atrazine dimers. The partial dimerization constants are also used to measure the effect of a CF3 label on hydrogen bonding and to show that dimerization constants can be obtained from either 19F NMR or 1H NMR data. The CF3 label enhances the hydrogen-bond donating ability of adjacent NH protons by about 20%, resulting in a higher dimerization constant for CF3-labeled atrazine (86±10 M-1) compared to that for atrazine (62±16 M-l).


Barak, P. and Y. Chen. 1992. Equivalent radii of humic macromolecules from acid-base titration. Soil Sci. 152:184-195.

The macromolecular nature of humic substances is well established, and cylindrical geometry appears most likely although molecular dimensions have not been published. Previous analyses of acid-base titrations of humic acids have largely ignored the macromolecular nature of the humic molecule and the effect of ionization of titrated groups on the hydronium ion concentration in the vicinity of untitrated groups. In this work, humic macromolecules are modeled as cylinders with surface potentials generated by the ionization of acidic groups. Based on data collected from e titrations of two humic acids at ionic strengths between 0.001 and 0.100 M NaCl and numerical solutions of the Poisson-Boltzmann equation for surface potentials, the radii of ideal charged cylinders that would display the same titration behavior in response to humic charge density and ionic strength were calculated. The results of these calculations show that humic macromolecules have equivalent radii ranging from about 1.1 nm at 10% ionization to 0.24 nm at 90% ionization. This change in equivalent radius may be conceptualized as the quantitative expression of changes in configuration as a result of uncoiling and extension due to electrostatic repulsion among charged groups on the same molecule. The derived charge densities reach relatively constant values of 1.3 to 1.5 x 104 esu cm-2 at 50 to 90% ionization. The data also support the concept of at least two different weakly acidic groups with different acid strengths or a Gaussian distribution of acidic groups, about a central pK value.


Bouabid, R., E.A. Nater, and P. Barak. 1992. Measurement of pore size distribution in a lamellar Bt horizon by epifluorescence microscopy and image analysis. Geoderma 53:309-328.

A staining technique suitable for epifluorescence microscopy of polished block surfaces was developed using proprietary dyes (Sanford Co.). The dyes greatly enhanced the contrast between particles and pores, thereby allowing, with only minimal processing, the production of images suitable for automated pore and particle size measurements.

An algorithm, the "multi-directional minimum chord" (MDMC) method, was developed for measurement of pore size as it relates to the hydraulic properties of soils. Pore chord lengths were measured in two or more directions through a set of points on a grid. The smallest dimension was retained as being most representative of the effective capillary diameter, or hydraulic diameter, of the pore. Chord length distributions measured by the MDMC method were compared to those obtained by the unidirectional chord intercept method.

These techniques were applied to a study of lamellar Bt horizon formation in sandy glacial outwash in the Anoka Sand Plain, Minnesota, U.S.A. The lamellae are nearly horizontal, occur from 0.6 to >2m depth, and vary in thickness from 0.5 to 6 cm. It was hypothesized that differences in pore size distribution initially present in the sands caused changes in soil hydraulic properties that may have been responsible for the initial formation of lamellae. Undisturbed samples containing lamellae and the underlying interlamellar horizons were collected using Kubiena boxes, oven dried at low temperature, cast in resin, sawed in half, polished, and stained. Digitized images of lamellae and the uppermost part of the interlamellar horizons were taken using epifluorescence microscopy and then edited to remove clays to simulate conditions present before the formation of the lamellae.

Pore and particle size distributions measured on the images by the MDMC method showed that significant differences existed between the lamellae and the uppermost part of the underlying interlamellar horizons. In all cases a coarser over finer pore size discontinuity existed at the bottom of the lamellar horizon, in support of the proposed mechanism for the initiation of lamellae formation.


Hadas, A., M. Sofer, J.A.E. Molina, P. Barak, and C.E. Clapp. 1992. Assimilation of nitrogen by soil microbial population: NH4 vs. organic N. Soil Biol. Biochem. 24:137-143.

Nitrogen assimilation by microbial biomass during the decay of organic material in soil may follow two patterns: (I) direct assimilation of low molecular weight organic N compounds (Direct hypothesis) or (2) immobilization of mineral N, while organic N is completely mineralized (MIT hypothesis). To test these hypotheses equal concentrations of NH4-N and alanine-N were added to soils, either one or the other labeled with 15N, and incubated for 1.2 days. The K2SO4-extractable organic and mineral N and 15N and CO2 release were measured periodically. Experimental results were compared with data computed by two versions of the model NCSOIL, that simulates the C-N turnover and 15N distribution among soil pools, and is structured to represent either the Direct or the MIT hypothesis. The fitted first order rate constant of mineralization of alanine was 3.2d-1, following a delay of 0.25d. Evolution of CO2 proceeded at a considerable rate after alanine was decomposed and net N mineralization had ceased, indicating a rapid decomposition of the microbial population that consumed alanine. The isotopic dilution of mineral N proceeded very rapidly and fitted the simulation by MIT better than by the Direct model. The rate of 15N withdrawal from total extractable N was greater when alanine was labeled and fitted the prediction by the Direct model, but when NH4 was the source of 15N, the Direct model failed to predict 15N consumption. It seemed that both pathways operated concurrently, with the Direct dominating N assimilation by the substrate specific population and the MIT operating at the level of the native soil population.


Laird, D.A., P. Barak, E.A. Nater, and R.H. Dowdy. 1991. Chemistry of smectitic and illitic phases in interlayered soil smectite. Soil Sci. Soc. Am. J. 55:1499-1504.

The objective of this investigation was to determine the elemental composition and mineralogy of the smectitic and illitic phases in interstratified smectite-illite from a typical upper Midwestern agricultural soil. A sample of soil clay (<2-um fraction) from the Ap horizon of a Webster (fine-loamy, mixed, mesic Typic Haplaquoll) pedon was fractionated by centrifugation to prepare various fine-clay (<0.020-, <0.026-, <0.036-, <0.045-, <0.060-, and <0.090-µm size fractions) samples. X-ray diffraction analyses indicated that interstratified smectite-illite was the only mineral present in significant quantities in the fine-clay samples. Elemental analyses of the fine-clay samples were performed by inductively coupled plasma-atomic emission spectroscopy using suspension nebulization. The elemental analyses revealed significant linear correlations for the K vs. other element relationships (P < 0.001 for K vs. Si, Al, Fe, Ca, Ti, Mn, and Zn, and P < 0.01 for K vs. Mg). A nonlinear parameter optimization technique, based on elemental mass balance, was used to estimate the elemental compositions and proportions of the smectitic (K-free) and illitic (K-bearing) phases in the fine-clay samples. The results for the elemental mass balance optimization were independently verified by water mass balance. The smectitic phase was a high-charge (0.482 per formula unit), Fe-rich montmorillonite (46.6% tetrahedral charge). The illitic phase consisted of dioctahedral, tetrahedrally charged (86.9% tetrahedral charge) elementary illite particles. Layer charge for the illitic phase was 0.473 per formula unit, which is substantially below the lower limit for classification of illite. The interstratified smectite-illite comprised at least 60% of the whole (<2-um fraction) soil clay and the illitic phase comprised at least 36% of the interstratified smectite-illite.


Baruch, E., D. Lichtenberg, P. Barak, and S. Nir. 1991. Calcium binding to bile salts. Chem. Phys. Lipids 57:17-27.

Calcium binding to bile salt monomers and micelles is an important issue with respect to the possible (but rare) precipitation of calcium bile salts in the gallbladder. In the present work the binding of Ca2+ to six bile salts was measured in solutions containing 2 to 100 mM bile salts by means of a calcium-sensitive dye, murexide, which determines the ionic calcium concentration. In solutions containing bile salt at concentration higher than 20 mM most, if not all, of the bound Ca2+ is associated with micellar surfaces. The results were analyzed by employing a model which combines specific binding with electrostatic equations and accounts for the system being a closed one. The analysis of Ca2+ binding data considered explicitly the presence of Na+ ions and yielded intrinsic binding coefficients for Ca2+ and Na+ which were utilized to explain and predict binding results for various concentrations of Ca2+, Na+ and bile salts. The calculations indicate that in saline solutions most of the surface sites were bound by Na+, whereas less than 10% were bound by Ca2+ even in the presence of 8 mM Ca2+. The binding of Ca2+ to bile salt micelles increases with pH. An increase in temperature results in reduced binding affinity of Ca2+ to the bile salt micelles.


Barak, P., Y. Coquet, T. Halbach, and J.A.E. Molina. 1991. Evaluation of the biodegradability of polyhydroxybutyrate(co-hydroxyvalerate) and starch-incorporated polyethylene plastic films in soils. J. Environ. Qual. 20:173-179.

Given the extremely low rates of microbial decomposition of most common plastics, the manufacture of biodegradable plastics is of interest as a means of managing the solid waste stream, as well as for specialty applications in pharmaceuticals and agriculture. In order to evaluate the biodegradability of several plastics commercially developed for enhanced biodegradability, plastic films of two types-- (I) polyhydroxybutyrate copolymerized with hydroxyvalerate (PHBV) and (ii) low density polyethylene (LDPE) incorporated with a starch filler were incubated for 44 d under moist, aerobic conditions in two soils, an acid sand and a calcareous sandy loam. Biodegradability of the plastics was evaluated based on evolution of CO2-C upon incubation and by microscopic examination after 44-and 150-d incubation under the same conditions. Biodegradation of polyhydroxybutyrate films ranged from 5% to near complete biodegradation during the 44-d incubation, depending on soil type, film thickness, and the nature of chemical additives to the polymer. Granules of embedded starch exposed at the surface of starch-incorporated polyethylene films were degraded within 14 d, after which no further biodegradation could be detected; no gross deformations of the plastic film were associated with the loss of surface starch.


Barak, P., J.A.E. Molina, A. Hadas, and C.E. Clapp. 1990. Mineralization of amino acids and evidence of direct assimilation of organic nitrogen. Soil Sci. Soc. Am. J. 54:769-774.

Rival hypotheses, the mineralization-immobilization-turnover (MIT) hypothesis and the direct hypothesis, contend that deamination of soluble, low-molecular-weight nitrogenous compounds in soil is mediated by either extracellular or intracellular enzymes, respectively. To test these hypotheses, two amino acids, glycine (C/N = 1.7) and leucine (C/N = 5.2), were added to an acid Hubbard loamy sand (sandy, mixed Udorthentic Haploboroll) and incubated for 7 d. Net mineralization of both C and N were S-shaped functions of time, indicating that simple first-order substrate-dependent kinetics were not applicable. The net mineralization of C and N were strongly correlated with each other and reflect the C/N ratio of the substrate and the C/N ratio and microbial efficiency of the microbial biomass. Labeled 15N data, when analyzed using kinetic models reflecting either the direct or MIT hypotheses, reject the MIT hypothesis (alpha = 0.01) and show evidence of direct incorporation of amino acids into the microbial biomass.


Barak, P., J.A.E. Molina, A. Hadas, and C.E. Clapp. 1990. Optimization of an ecological model with the Marquardt algorithm. Ecol. Modelling 51:251-263.

Optimization of parameters in ecological models can present many challenges, including multiple dependent variables on which to calculate fit, slowly converging search algorithms, nonanalytical derivatives, parameters constrained by their physical meaning in the model to a given sign or range, and excessively long run times for optimization calculations. The Marquardt algorithm has been restructured and an appropriate figure-of-merit function formulated to address these problems. As an example, a soil nitrogen and carbon transformation simulation model (NCSOIL) may be optimized for two and three unknown parameters within ten iterations or less, based on initial guesses of parameter values in error by an order of magnitude.


Barak, P. 1990. SPECIES: A spreadsheet program for modeling speciation of soil solution. J. Agron. Educ. 19:44-46.

The SPECIES program is a solution equilibrium model to teach concepts of ion activity and ion speciation as applied to soil solutions. The program is written as a spreadsheet file that may be used with Lotus 1-2-3 or compatible spreadsheet software. The spreadsheet format provides a user-friendly computer environment and leaves the computational portions of the program transparent to the user. Results are easily manipulated on screen, exported to disk, or output as hard copy using standard spreadsheet functions.


Barak, P. 1989. Double layer theory prediction of Al-Ca exchange on clay and soil. J. Colloid Interface Sci. 133:479-490.

The Poisson-Boltzmann equation was solved numerically for the case of a diffuse electric double layer containing mixed divalent and trivalent electrolytes. The predicted Gapon selectivity coefficient was found to range over two orders of magnitude while the Vanselow selectivity coefficient changed by 10% over the range of ionic ratios considered. The formation of tactoids should increase the affinity of the exchanger for cations with higher ionic charge. Ionic strength has little effect on predicted selectivity coefficients. The results of double layer calculations approximated, but systematically deviated from, two sets of published values for Al3+-Ca2+ exchange on montmorillonite. Consideration of the speciation of Al3+, particularly including the dimer Al2(OH)24+, improved the agreement between predicted values and published results. Predicted cation exchanger composition is in agreement with published base saturation data for mineral soils.


Last modified 25 Oct 2013 by Phillip Barak (pwbarak@wisc.edu)