Advances in agronomy volume 99

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CONTRIBUTORS Numbers in Parenthesis indicate the pages on which authors contributors begin V C Baligar (345) USDA-ARS-Sustainable Perennial Crops Lab, Beltsville, Maryland 20705-2350 Guilhem Bourrie´ (227) INRA, UR 1119, Soil and Water Geochemistry, Europoˆle de l’Arbois, B.P 80, F-13545 Aix-en-Provence (France) J F Briat (183) CNRS, Universite´ Montpellier II, SupAgro, INRA, UMR5004 ‘Biochimie et Physiologie Mole´culaire des Plantes’, Place Pierre Viala, F-34060 Montpellier cedex I, France N K Fageria (345) National Rice and Bean Research Center of EMBRAPA, Caixa Postal 179, Santo Antoˆnio de Goia´s, GO, CEP 75375-000, Brazil Rebecca E Hamon (289) Plant Chemistry Section, Agricultural and Environmental Chemistry Institute, Faculty of Agricultural Sciences, Universita` Cattolica del Sacro Cuore, Via Emilia Parmense 84, I-29100, Piacenza, Italy Alfred E Hartemink (125) ISRIC - World Soil Information, 6700 AJ Wageningen, The Netherlands P Hinsinger (183) INRA, SupAgro, UMR1222 ‘Bioge´ochimie du Sol et de la Rhizosphe`re’, Place Pierre Viala, F-34060 Montpellier cedex 1, France Philip M Jardine (1) Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 P Lemanceau (183) INRA, Universite´ de Bourgogne, UMR1229 ‘Microbiologie du Sol et de l’Environnement’, CMSE, BV 86510, F-21034 Dijon cedex, France Enzo Lombi (289) Plant and Soil Science Laboratory, Department of Agricultural Science, Faculty of Life Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark ix x Contributors J M Meyer (183) CNRS, Universite´ Louis Pasteur, UMR7156 ‘De´partement Environnement, Ge´ne´tique mole´culaire et Microbiologie’, F-67000 Strasbourg, France David R Parker (101, 289) Soil and Water Sciences Section, Department of Environmental Sciences, University of California, Riverside, California 92521 A Robin (183) INRA, Universite´ de Bourgogne, UMR1229 ‘Microbiologie du Sol et de l’Environnement’, CMSE, BV 86510, F-21034 Dijon cedex, France Angelia L Seyfferth (101) Department of Environmental Sciences, University of California, Riverside, California 92521 Fabienne Trolard (227) INRA, UR 1119, Soil and Water Geochemistry, Europoˆle de l’Arbois, B.P 80, F-13545 Aix-en-Provence (France) G Vansuyt (183) INRA, Universite´ de Bourgogne, UMR1229 ‘Microbiologie du Sol et de l’Environnement’, CMSE, BV 86510, F-21034 Dijon cedex, France PREFACE Volume 99 contains seven comprehensive and timely reviews dealing with plant, soil, and environmental sciences Chapter is an excellent review on the influence that complex hydrological, geological, and biological processes have on inorganic contaminant fate and transport, with emphasis on field-scale studies Chapter focuses on the uptake and fate of perchlorate in plants Chapter is a timely review on the soil and environmental issues related to the use of sugarcane for bioethanol production Chapter is a comprehensive review on iron dynamics in the rhizosphere including the impact of plants and microorganisms on iron status and iron-mediated interactions in the rhizosphere Chapter deals with a reevaluation of the Fe cycling in soils in light of recent advances in understanding the geochemistry of green rusts and fougerite Chapter is a thorough review of recent advances on using isotopic dilution techniques in trace element research including a discussion of methods, benefits, and limitations Chapter deals with liming of tropical Oxisols and includes factors affecting lime requirements and methods and frequency of lime applications I thank the authors for their fine contributions DONALD L SPARKS University of Delaware xi C H A P T E R O N E Influence of Coupled Processes on Contaminant Fate and Transport in Subsurface Environments Philip M Jardine Contents Introduction and Rationale Chapter Objectives and Outline General Overview on the Impact of Coupled Processes on Subsurface Fate and Transport 3.1 The importance of subsurface media structure 3.2 Influence of subsurface hydrologic processes on biogeochemical reactions 3.3 Influence of the subsurface capillary fringe on couple hydro-bio-geochemical reactions Influence of Coupled Processes on Inorganic Contaminant Fate and Transport 4.1 General overview 4.2 Inorganic metals 4.3 Inorganic radionuclides 4.4 Inorganic ligands 4.5 General inorganics 4.6 Modeling coupled processes involving dissolved aqueous phase inorganic constituents Influence of Coupled Processes on Organic Contaminant Fate and Transport 5.1 General overview 5.2 Chlorinated solvents 5.3 Hydrocarbons 5.4 Pesticides and herbicides 5.5 Modeling coupled processes involving organic constituents Concluding Remarks Acknowledgments References 4 10 10 11 24 34 40 44 48 48 51 57 65 67 70 73 73 Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 Advances in Agronomy, Volume 99 ISSN 0065-2113, DOI: 10.1016/S0065-2113(08)00401-X # 2008 Elsevier Inc All rights reserved Philip M Jardine Abstract The following chapter emphasizes subsurface environmental research investigations over the past 10 to 15 years that couple hydrological, geochemical, and biological processes as related to contaminant fate and transport An attempt is made to focus on field-scale studies with possible reference to laboratory-scale endeavors Much of the research discussed reflects investigations of the influence of coupled processes on the fate and transport of inorganic, radionuclide, and organic contaminants in subsurface environments as a result of natural processes or energy and weapons production endeavors that required waste disposal The chapter provides on overview of the interaction between hydro-biogeochemical processes in structured, heterogeneous subsurface environments and how these interactions control contaminant fate and transport, followed by experimental and numerical subsurface science research and case studies involving specific classes of inorganic and organic contaminants Lastly, thought provoking insights are highlighted on why the study of subsurface coupled processes is paramount to understanding potential future contaminant fate and transport issues of global concern Introduction and Rationale Until recently, worldwide waste disposal practices were an afterthought to the desire for economic expansion and national security and defense In an age full of fear, greed, and the desire for global superiority, waste disposal practices regarding weapons, energy, and food production, and the quest for a higher standard of living, were of little consequence and were deemed an effort that future generations would confront Unfortunately, cleanup technologies have been slow in development and the resolution of the legacy waste problem persists An excellent example exists within several government agencies within the United States (U.S.) such as the Department of Energy (DOE) and the Department of Defense (DoD) which face a daunting challenge of remediating huge below ground inventories of legacy radioactive, toxic metal, and mixed organic wastes The scope of the problem is massive, particularly in the high recharge, humid regions east of the Rocky Mountains, where the off-site migration of contaminants continues to plague soil water, groundwater, and surface water sources Even in semiarid regimes west of the Rocky Mountains, the threat of contaminant migration through seemingly ‘‘dry’’ porous media persists due to slow water movement along fine sediment layers as a result of tension-driven anisotropic flow Industrial activities have also contributed to massive legacy waste problems that are associated with accidental and intentional spills and disposal activities The cleanup of these activities by DOE, DoD, and the U.S Environmental Protection Agency (EPA) has Influence of Coupled Processes on Contaminant Fate been ongoing for several decades with the pace slowing due to budget cuts and priority shifts in the U.S government spending portfolio In this context, it is not surprising that determining the best course of action— large-scale cleanups, focused hotspot remediation, or no action (natural attenuation)—remains exceedingly difficult from a technical standpoint If a natural system has sufficient capacity for clean-up of contaminants by in situ processes (e.g., adsorption, dilution, precipitation, biodegradation, chemical transformation), perhaps natural attenuation processes should be considered as the first option The current reality (i.e., 2008) is that contaminated sites are closing rapidly and many remediation strategies have chosen to leave contaminants in-place with little consideration of whether the decision is appropriate In situ barriers, surface caps, and bioremediation are often the remedial strategies of choice By choosing to leave contaminants in-place, we must accept the fact that the contaminants will continue to interact with subsurface and surface media Contaminant interactions with the geosphere are complex and investigating long-term changes and interactive processes is imperative to verifying risks Since contaminants may be left in-ground, it is critical to understand immobilization and remobilization processes that may operate during long-term stewardship as it is our societal responsibility to ensure a healthy environment for future generations A deeper understanding of the relevant spatial and temporal scales that govern the fate of transport mechanisms is needed in order to make informed decisions about the applicability of various remediation options including natural attenuation Understanding the spatial and temporal scales at which coupled hydrobio-geochemical processes operate is essential to designing an efficient and effective monitoring program for long-term stewardship Chapter Objectives and Outline In the following chapter we emphasize subsurface environmental research investigations that combine hydrological, geochemical, and biological processes as related to contaminant fate and transport We not consider coupled subsurface deformation, mechanical, or thermal processes as related to chemical distribution and reactivity This information can be found in Bai and Elsworth (2000) We attempt to discuss only fieldscale studies with possible reference to laboratory-scale endeavors A review of environmental investigations involving coupled processes at the laboratory scale can be found in Geesey and Mitchell (2008) Much of the research discussed in this chapter reflects investigation of the influence of coupled processes on the fate and transport of contaminants in subsurface environments as a result of natural processes or energy and weapons production endeavors that require waste disposal Many of the approaches and research Philip M Jardine findings from these studies have potential application to future investigations on the environmental consequences of contaminant dissemination as a result of shifts in energy and climate policy and man-made changes to the global hydrologic cycle Section provides an overview of the interaction between hydrological, geochemical, and microbial processes in structured, heterogeneous subsurface environments and how these interactions control contaminant fate and transport Next, Section highlights recent field relevant research on the influence of these coupled processes on inorganic contaminant fate and transport, and Section provides numerous examples of field-scale research on the impact of coupled processes on organic contaminant fate and transport Lastly, Section provides concluding remarks of how the study of subsurface coupled processes is paramount to understanding potential future contaminant fate and transport issues of global concern General Overview on the Impact of Coupled Processes on Subsurface Fate and Transport 3.1 The importance of subsurface media structure Undisturbed subsurface soils and geologic material consist of a complex continuum of pore regions ranging from large macropores and fractures at the millimeter scale to small micropores at the submicrometer scale Structured media, common to most subsurface environments throughout the world, accentuates this physical condition which often controls the hydrological, geochemical, and microbial processes affecting transport phenomena More often than not, subsurface media structure controls the rate and extent of geochemical and microbial reactions, all of which ultimately influence contaminant fate and transport processes Geochemical and biological reactions and activity may, in turn, influence media structure and the hydrodynamics of the system (e.g., biogeochemical pore plugging, earthworm channels) Therefore, the extent and magnitude of subsurface biogeochemical reactions is often controlled by the spatial and temporal variability of the media structure which controls the system hydrodynamics The physical properties of the media (e.g., structured, layered) coupled with its antecedent water content and the duration and intensity of precipitation events, dictate the avenues of water, solute, and microbe movement as well as their interaction within the subsurface In humid environments where structured media is commonplace, transient storm events invariably result in the preferential migration of water (Gerke et al., 2007; Hornberger et al., 1991; Jardine et al., 1989, 1990a,b; 1998, 1999a, 2001, 2002; 2006, 2007; Mayes et al., 2003; Shaffer et al., 1979; Shuford et al., 1977; Vogel et al., 2006; Wilson et al., 1989, 1993, 1998) Influence of Coupled Processes on Contaminant Fate Highly conductive voids within the media (e.g., fractures, macropores) carry water around low permeability, high porosity matrix blocks or aggregates resulting in water bypass of the latter (Fig 1A) Subsurface preferential flow is also a key mechanism controlling water and solute mobility in arid environments (Hendrickx and Yao, 1996; Ho and Webb, 1998; Liu et al., 1998; Mayes et al., 2003, 2005; Pace et al., 2003, 2007; Porro et al., 1993; Ritsema et al., 1993, 1998; Tompson et al., 2006) Lithologic discontinuities and sediment layering promote perched water tables and unstable wetting fronts that drive both lateral and vertical subsurface preferential flow (Fig 1B) Water that is preferentially flowing through media often remains in intimate contact with the porous matrix, and physical and hydrologic gradients drive the exchange of mass from one pore regime to another Mass exchange is time dependent and is often controlled by diffusion to and from the matrix The preferential movement of water and mass through the subsurface therefore significantly impacts geochemical and microbial processes by controlling the extent and rate of various reactions with the solid phase It imposes kinetic constraints on biogeochemical reactions and limits the surface area of interaction by partially excluding water and mass from the matrix porosity These concepts are likewise conveyed in the subject area hydropedology which provides a link between the disciplines of pedology (e.g., soil B A cm 10 cm Structured saprolite Laminated sediments Figure An example of structured media from (A) humid and (B) semiarid climatic regimes showing a fractured shale-derived saprolite and a layered sediment consisting of laminated coarse- and fine-grained material, respectively The fractured saprolite in (A) consists of macroporous fast-flowing fractures that surround low permeability, high porosity matrix blocks The laminated sediments in (B) are irregularly spaced depositional layers of fine- and coarse-grained minerals that have drastically different hydrologic characteristics that often results in tension-driven anisotropic lateral flow along fine layers Philip M Jardine macro- and micromorphology) and subsurface hydrology and other disciplines involved with land, air, and water interfaces (Kutilek and Nielsen, 2007) The coupling of such processes suggests that anisotropy is a general characteristic of soils and that the formulation of physically meaningful transport parameters requires quantitative knowledge of soil micromorphology As suggested by Kutilek (1978, 1990), the assumption that soil is an isotropic body is only an approximation of reality Coupling of hydropedology with geochemistry and microbiology provides new insights into the role of solute and contaminant fate and transport as a function of hydrology and soil structure 3.2 Influence of subsurface hydrologic processes on biogeochemical reactions Subsurface geochemical and microbial reactions are directly linked to the system hydrodynamics Soil moisture conditions that promote the onset of preferential flow and thus higher volumetric flux per unit area will minimize geochemical and microbial interfacial reactions due to decreased residence times during transport and potential bypass of the soil matrix (Estrella et al., 1993; Jardine et al., 1988, 1993a; Jarvis, 2007; Jarvis et al., 2007; Kung, 1990a,b; Maraqa et al., 1999) Conversely, soil moisture conditions that not promote preferential flow will, in general, enhance geochemical retardation and microbial interfacial reactions In the presence or absence of preferential flow, water content variations affect the extent and rate of geochemical and microbial reactions very differently The extent of contaminant retardation by the solid phase via geochemical mechanisms (e.g., sorption, redox alteration, and complexation) will be more pronounced when flow is restricted to smaller pore size regimes (e.g., mesopores/micropores) Jardine et al (1988, 1993a,b) have found that the reactivity of reactive contaminants and chelated radionuclides increased dramatically with a slight decrease in pressure head or water content The larger surface area and potential reactivity of smaller sized pores versus macropores allow geochemical reactions to proceed to a more significant extent in the subsurface media Microbial activity and transport in the subsurface are also controlled by physical and chemical interactions with the solid phase as well as the availability of nutrients, sources of carbon, and possible electron acceptors Hydraulic conductivities can have a severe influence on nutrient transport and delivery within the subsurface and can often be the most limiting aspect of bioremediation Biotransformation, biosorption, and electron transfer reactions are typical processes that govern the fate and transport of microbes in the subsurface Unlike solutes that can reside within nearly all of the pore structure of subsurface media, microbes (i.e., bacteria and viruses) are too large to reach a significant fraction of the micropore regime and are restricted to the mesopore and macropore domains Usually, less than 5–10% of the 392 N K Fageria and V C Baligar Fageria, N K (1992) ‘‘Maximizing Crop Yields.’’ Marcel Dekker, New York Fageria, N K (2000) Upland rice response to soil acidity in cerrado soil Pesq Agropec Bras 35, 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contamination, 12–13 removal, 13–14 microbial activity, 14–15 sources and uses, 11 Arsenicicoccus bolidensis, 15 Atrazine herbicides, 156 B Bacterial antagonism, plant health, 205–207 Benzene, toluene, ethylbenzene, and xylene (BTEX), 68 contamination and biodegradation, 60–61 and Fe reduction, 61–62 microbial degradation, 62 Bioaccumulation, 16–17, 19 Bioavailable iron, definition, 192 Bioenergy, definition, 126 Bioethanol production, 154–155, 161–162 Biofuel crop, sugarcane cultivation global production, 127–128 trash and green harvesting, 128 Biological nitrogen fixation (BNF), 146 Bioremediation, BTEX contaminants, 61 chlorinated solvents, 52–53, 55 limiting factor, 6–7 organic contaminant, 50 selenium, 21 technetium, 32–33 uranium, 25–28 Biotransformation, 6, 13, 64 Brevibacillus sp., 29 Buffering capacity, soil, 376 C Canadian Forces Base (CFB), 63 Capillary fringe, 8–10 Chemical kinetic and equilibrium model (KEMOD), simulation model, 67 Chlorinated aliphatic hydrocarbons (CAHs), 51, 57 Chlorinated solvents C isotope technique, 55 coupled processes influence, 52–53 microbial-mediated dechlorination, 56–57 subsurface migration of, 51–52 TCE biodegradation, 53–54 TEAP variations, 54–55 Chloroform (CF), 51, 57 Chromium (Cr), 22–24 Coal-tar creosote, 62–64 Coca ColaÒ , 290 Colloidal interferences, 320–321 Community amplified ribosomal DNA restriction analysis (ARDRA), 56 Coupled processes, subsurface environments BIOMOC and UCODE, 68 BTEX, 60–62 coal-tar creosote, 62–64 crude oil, 57–60 CRUNCH and FERACT model, 46 DNAPL transport, 51–53 3D numerical model, 68 herbicide degradation, 66–67 HYDROGEOCHEM model, 45–46 hydrologic processes geochemical reactions, microbial activity, 6–8 landfills, 40–42 metal contaminants arsenic (As), 11–15 chromium (Cr), 22–24 mercury (Hg), 15–20 selenium (Se), 20–22 MODFLOW model, 47 MT3D99 model, 67–68 nitrate in groundwater contamination, 35–37 nitrogen cycle, 34–35 radioactive waste, 38–39 401 402 Index Coupled processes, subsurface environments (cont.) perchlorate, 39–40 permeable reactive barriers, 42–44 pesticides fate and transport, 65–66 PFLOTRAN model, 69 radionuclide contaminants strontium (Sr), 33–34 technetium (Tc), 32–33 uranium (U), 24–32 RPARSim/KEMOD model, 67 Crop rotation, 368–369 Crude oil, 57, 59, 61, 68 65 Cu spiking, 308–309 D Denaturing gradient gel electrophoresis (DGGE), 56 Dense nonaqueous phase liquids (DNAPLs), 51–52, 62, 67 Department of Defense (DoD), 2, 24, 55 Department of Energy (DOE), Hg dissemination, 15 nitrate waste plumes, 38–39 remediation below ground inventories, strontium, 34 technetium, 32–33 uranium, 24–25 Desulfovibria spp., 30 Dichloroelimination, 51 Diffusion gradients in thin films (DGT), 292 Dissimilatory iron reducing bacterium (DIRB), 278–279 E Enterobacter cloacae, 22 E-value determination, isotopic dilution methods accuracy and precision, 314–315 equilibration time, 310–313 interpretation metal uptake or toxicity, 326 usefulness, 327 isotope fixation, 317 schematic representation, 311 suspension matrix choice, 309–310 F Fenton chemistry, 202 Fe(III)-reducing bacteria (FeRB), 26, 29–30, 56 Ferrihydrite biotransformation, 278–279 solubility, 188, 190 Ferritin, 202 Fertilizer denitrification, 141–142 Fluorescent pseudomonads See Pyoverdines Fougerite mineral citrate-bicarbonate (CB) extraction of, 241–242 ferrous doublet in, 240 geochemical and structural constraints of, 264–265 geochemical significance, 280–281 identification, XRD spectra decomposition criteria and characteristics, 262 decomposition peak results, 254–260 interlayer anion in fougeres–fougerite, 260–261 material and methods, 254 Mg-saturated samples in, 260 structural characterization, 247, 252–253 ternary solid solution model, 261–263 G Geobacteraceae, 25–26, 29 Geobacter spp., 30–31 Geochemical transport models inorganic contaminants CRUNCH and FERACT, 46 HYDROGEOCHEM and HBGC123D, 45–46 MODFLOW, 47 organic contaminants BIOPLUME III and KEMOD, 67 3D numerical model, 68 MT3D99 67–68 PFLOTRAN, 69 GeoChip, 30 Gibbs free energy, 265–266 Gleyey soil, iron marker field tests, 231–233 rH measurements Ag/AgCl electrode, 235–236 electron potential, 233–234 Nernst’s law, 237 soil color, 229–231 Goethite DCB and CB for, 242 and DIRB, 279 physical properties, 240 redox interactions, 273 Green rusts (GRs) See also Fougerite mineral; Synthetic green rusts formation, DIRB, 278–279 green rust1 (GR1) crystal structure, 248 interplanar distances and intensities, 249–250 layer-to-layer and interatomic distances, 252 reduced coordinates of atoms, 251 stacking sequences and interlayered anions, 246, 248 403 Index green rust2 (GR2) crystal structure, 248 interlayered anions, 252 and metals, 228 nitrate reduction mechanism, 276–277 pH, 273–274 seasonal dynamics, 274–276 redox interactions electron potential and pH, 271–272 Fe(II)–Fe(III) hydroxides in, 273 selenate reduction, 277–278 solid solution model chemical potential estimation, 263, 269 fougerite estimation, 270 H Herbicides degradation, 66–67 environmental impact, 157 leaching of, 157–158 macrofauna, 152 and pesticides, 156–158 Humic substances, 191–192 Hydrogen ion activity See Soil pH Hydrogenolysis, 51 Hydroxychloride green rust, 248 I Icenucleation activity See Bioavailable iron Inorganic fertilizers effects of microbial biomass, 153 on sugarcane yield, 140 heavy metals and rare earth elements, 160 nitrogen fertilizer, 158–159 phosphorus fertilizer, 159 recovery of, 143 Iron (Fe) acidification, 194–197 bioavailability, 192–193 biological properties, 185–186 chemical properties chelation and complex formation, 190–191 iron oxides solubility, 188–190 oxidation, 188 concentration of, 186 dynamics, 187 ferritin, homeostasis, 202 interactions in rhizosphere bacterial antagonism, 205–207 Fusarium oxysporum role, 203–204 plant nutrition, 207–208 pyoverdin-mediated iron uptake, 204–205 thermodynamic and kinetic constraints, 209 nutrient bioavailability, 193 oxides solubility, 188–190 uptake strategy Fe(III) reduction, 200–201 phytosiderophores role, 197–199 siderophores and pyoverdines, 199–200 Iron, redox geochemistry See also Green rusts (GRs) chemical extraction citrate-bicarbonate (CB) reagent, 241 dithionite-citrate-bicarbonate (DCB) reagent, 240–241 soil profile, 242 soil solids iron characterization, 239–242 sample conditioning, 239 soil solutions characterization of, 238–239 Fe control, 269–270 mobility and seasonal dynamics, 242–246 nitrate dynamics, 274–276 sampling, 238 Isotopically exchangeable kinetic (IEK) method, 310–313 Isotopic dilution methods accuracy and precision in, 314–315 colloidal interferences, 320–321 and equilibration time, 310–313 error propagation, 317–318 E-value determination interpretation of, 325–327 schematic representation for, 311 suspension matrix choice, 309–310 HVG-AAS determination of Se, 319 isotope choice, 306–307 L-value determination Cd and Zn E-and L-values, 328–331 deposition rates in, 333 methodological sources of error, 333–334 mixing method, 320 seed/juvenile contribution, 318–319 oxidation state changes arsenic redox conditions, 322 equilibration time, 323–324 PIE and E-value (Etot) 321–323 As and Se elements, 325 principle E-and L-value procedures, 294–295 exchangeable pool assessement, 296–305 and soil contaminants, 293 solution equilibrium models, 335 spike-derived artifacts and isotope fixation, 317 206 Pb spike values, 316 spiking for, 308–309 uses of speciation techniques, 336 404 Index L Lepidocrocite bioreduction, 279 oxidation of green rust, 261 physical properties, 240 Lime requirement, crop production applications of, 384–386 chemical analysis, 365–366 conservation tillage, 370–371 crop rotation, 368–369 crop species and genotypes, 371–372 definition, 364–365 nutrient interactions Ca2ỵ, Mg2ỵ, and Al3ỵ levels in, 374375 ion-ion, 372–373 types of, 373–374 organic manure benefits, 369–370 quantity determination aluminum saturation, 381–383 base saturation, 377–379 crop responses, 383–384 exchangeable ions, 379–381 soil pH, 376–377 soil fertility, 367–368 soil texture, 366–367 Liming method calcium and magnesium, role of, 353–354 disadvantages of, 363–364 heavy metals leaching and solubility, 358–360 improving soil structure, 360 mineral nutrition, 361–362 mycorrhizal colonization, 358 nitrous oxide mitigation, 362–363 nutrient use efficiency, 360–361 plant-beneficial microorganisms, 356–357 reducing phosphorus immobilization, 355–356 soil acidity amelioration, 350 Lolium perenne See Ryegrass plant L-value determination, isotope dilution methods consequences of, 313–314 mixing method, 320 seed/juvenile contribution, 318–319 vs E-values Cd and Zn, 328–331 deposition rates, 333 methodological sources of error, 333–334 M Macrofauna, fire ants, 152 Mercury (Hg) biogeochemical cycle, 16 emissions and toxicological effects, 15–16 in groundwater, 18 microbial activity, 17 migration processes, 17–18 speciation, 20 Metal contaminants arsenic (As), 11–15 chromium (Cr), 22–24 mercury (Hg), 15–20 selenium (Se), 20–22 Methylmercury (MeHg), 16–17, 19 Microbial biomass, 153–154 Miracle-GroÒ 118 Mycorrhizal colonization, 358 N Nernst’s law, 237 Neutralizing power, 366 Nitrate in groundwater contamination agricultural activities, 35–36 denitrification, 36–37 waste application, 37 nitrogen cycle, 34–35 radioactive waste, 38–39 Nitrification, 348 Nitrogen cycle, 34–35 Nitrogen (N) fertilizers application of, 137, 159, 167 gaseous losses efficiency of, 142 fraction of, 141 recovery of, 143 leaching, 140–141, 143, 158–159 Nitrous oxide (N2O) mitigation, 362 Nonaqueous phase liquids (NAPLs), 51 Nutrient balances, soil chemical properties agronomic variation, 144 biological nitrogen fixation (BNF), 145–146 denitrification, 145 O Organochlorine pesticides, 157 Oxisols definition, 352 occurence and distribution, 350–351 P Paenibacillus sp., 29 Perchlorate ions in environment conditions chemical properties, 102 natural occurrence of, 103–104 production of, 102–103 tetrahedral structure of, 103 phytodegradation, 111 in plants highly contaminated site assessment, 106–107 market survey assessment, 108–110 rhizodegradation, 111–112 405 Index toxicological issues analytical advancements in, 104 ecological effects, 106 human health effects, 105–106 uptake methodologies linear regression analysis, 117 phytoremediation, 110–112 surface adsorption, 119 temporal concentration data, 118–119 transpiration mechanism, 114–115 Perchloroethylene (PCE), 51 Permeable reactive barriers (PRB), 42–44, 47–48, 69 Pesticides erosion control, 151 and herbicides, 156–158 leaching of, 157–158 microbial biomass, 153 microbial degradation of, 64–66 pest management practices, 165 Petroleum, 57, 59–60 Phospholipids fatty acid (PLFA), 26 Phytodegradation, of perchlorate, 111–112 Phytoremediation under aerobic conditions, 111–112 anaerobic microcosms, 111 characterization of, 110 radio-labeled perchlorate detection, 112 Phytosiderophores iron uptake, 199 soil concentration of, 197 structures of, 198 Polycyclic aromatic hydrocarbons (PAHs), 62, 64 Potentially incorrect E-value (PIE), 321–323 Preharvest burning, sugarcane cultivation air pollution, 160–161 bioethanol production, 162 effects of, 165–166 greenhouse gas production, 155 loss of soil organic matter, 168 Pseudomonas fluorescens, 193 Pseudomonas stutzeri, 57 Pseudo-radial distribution functions (PRDF), 253 P spring effect, 355 pvd-inaZ, reporter gene, 204 Pyoverdines composition and synthesis, 199–200 iron uptake, 204–205 R Radio-labeled perchlorate, 112 Radionuclide contaminants strontium (Sr), 33–34 technetium (Tc), 32–33 uranium (U), 24–32 Redox-labile elements, 321 Rhizodegradation, 111–112 Rhizodeposition, 184–185 Rhizosphere iron-mediated interactions impact of plant health, 205–207 plant iron nutrients, 204–205, 207–209 soil’s chemical properties and microorganisms, 203–204 iron solubilization acidification, 195–197 chelation and complexation, 197–200 reduction, 200–201 Ryegrass plant, 331 S Selenate reduction, green rusts, 277–278 Selenium (Se), 20–22 Shewanella putrefaciens, 279 Siderophores See Phytosiderophores Soil acidity Al solubilization, 347–348 bacteria groups, 357 causes, 349 leaching method, 348 lime requirement, crop production applications of, 384–386 chemical analysis, 365–366 conservation tillage in, 370–371 crop rotation, 368–369 crop species and genotypes, 371–372 definition, 364–365 nutrient interactions, 372–375 organic manure benefits, 369–370 quantity determination, 376–384 liming method amelioration, 350, 352 calcium and magnesium role, 353–354 disadvantages of, 363–364 heavy metals leaching and solubility, 358–360 improving soil structure, 360 mineral nutrition, 361–362 mycorrhizal colonization, 358 nitrous oxide mitigation, 362–363 nutrient use efficiency in, 360–361 plant-beneficial microorganisms, 356–357 reducing phosphorus immobilization, 355–356 occurence and quantification, 347 Soil erosion control, 151 denitrification and nutrient losses, 145 soil compaction, 163 sugarcane cultivation, 149–150 Soil fertility, 367–368 Soil organic matter dynamics alfisols, 140 inceptisols and oxisols, 139–140 406 Soil organic matter dynamics (cont.) regression model, 138 systems of cultivation, 137–138 vertisols, 139 Soil pH, 376–377 Soil properties, sugarcane cultivation biological properties macrofauna, 152 microbial biomass, 153–154 chemical properties biological nitrogen fixation, 146 denitrification and volatilization, 141–142 different land-use system samples, 133–134, 136–137 inorganic fertilizers, 142 leaching, 140–141 monitoring, 129, 133–135 nutrient balances, 142–146 organic matter dynamics, 137–140 Type I and Type II data sources, 129 physical properties compaction and aggregate stability, 147–149, 163 soil erosion and control, 149–151 Soil texture, 366–367 Solid solution model, green rust chemical potential estimation, 263, 269 fougerite estimation, 270 Strontium (Sr), 33–34 Subsurface environments See also Coupled processes, subsurface environments capillary fringe, 8–10 future environmental issues, 70–72 geochemical and microbial reactions, 6–8 hydrologic processes geochemical reactions, microbial activity, 6–8 structured media, 4–6 terminal electron accepting processes hydrocarbon contamination, 54 recharge effects on, 55–56, 58–59 sewage-effluent plume, 54–55 zones, 48–49 Sugarcane cultivation bioethanol production, 154–155, 161–162 biofuel crop global production, 127–128 effects on air and water greenhouse gas emissions, 165 leaching, 164–165 preharvest burning, 165–166 environmental issues air quality, 160–161 herbicides, 156–157 impact on, 165 inorganic fertilizers, 158–160 pesticides and insecticides, 157–158 soil and water resource contamination, 155 Index water quality, 161 land-use system samples oxisols, 133 soil organic C contents, 136–137 Type II data, 134, 136 vertisol, 133–134 precision agriculture biofertilizers, 170 economic and ecological benefits of, 169 preharvest burning air pollution, 160–161 bioethanol production, 162 effects of, 165–166 greenhouse gas production, 155 loss of soil organic matter, 168 ratoon crop, 128 soil acidification, 137, 162–163 soil compaction, 147–149, 163 soil degradation, 137, 168 soil organic carbon contents, 165 soil pH, 134–137 sugarcane yields effects of continuous cultivation, 166 and soil changes, 168 soil fertility, 166–167 trash harvesting, 167–168 trash and green harvesting advantages and disadvantages, 164 soil organic matter dynamics, 137–140 Sugarcane monocropping systems, 169 Sulfate-reducing bacteria (SRB), 41, 57 Hg methylation, 20 TCE biodegradation, 53 technetium reduction, 33 uranium remediation, 26–28 Synthetic green rusts anions electronegativities and Gibbs free energies of, 265–266 green rust1 (GR1) crystal structure, 248 interplanar distances and intensities, 249–250 layer-to-layer and interatomic distances, 252 reduced coordinates of atoms, 251 stacking sequences and interlayered anions, 246, 248 green rust2 (GR2) crystal structure, 248 interlayered anions, 252 thermodynamic data, 266–269 T Technetium (Tc), 32–33 Terminal electron accepting processes (TEAPs), subsurface environments hydrocarbon contamination, 54 407 Index recharge effects on, 55–56, 58–59 sewage-effluent plume, 54 zones, 48–49 Thermodynamic modeling Gibbs free energy vs electronegativity, 265–266 solid solution composition, 264–265 ternary solid solution model, 261, 263 Thlaspi caerulescens, 328, 331 Trace elements adsorption and desorption methods, 291–292 fractionation methods, 290–291 isotopic dilution methods accuracy and precision, 314–315 colloidal interferences, 320–321 equilibration time, 310–313 isotope choice, 306–307 L-value determination, 313–314 oxidation state changes in, 321–325 principle of, 293–305 and soil contaminants, 293 spike-derived artifacts, 315–317 spiking for, 308–309 spectroscopic techniques, 292 Transpiration mechanism, perchlorate ions, 114–115 Trash and green harvesting, 128 advantages and disadvantages, 164 soil organic matter dynamics alfisols, 140 cultivation systems, 137–138 vertisols, 139 Trash management systems, 142 Trichloroethane (TCA), 51 Trichloroethylene (TCE) dechlorination, 54–55 DNAPL formation and transport, 51–52 groundwater degradation, 55 temporal variability, 53 U Uranium (U), 24 bioreduction, 31 bioremediation, 27–28 biotransformation analysis, 29–31 PLFA indicators, 26 reduction of U(VI), 25–26 US Environmental Protection Agency (EPA), 2, 102, 105–106 BIOPLUME III model, 67 MCL for arsenic, 12 nitrate, 35–36 perchlorate, 39 selenium effects, 21 X X-ray absorption near edge structure (XANES), 30 XRD spectra decomposition, Fougerite criteria and characteristics, 262 decomposition peak results, 254–260 interlayer anion in fougeres–fougerite, 260–261 material and methods, 254 Mg-saturated samples in, 260 Z Zero-tension lysimeters, 238 ... strategies are investigating techniques that decrease in- stream formation of methylmercury without having to further eliminate inorganic Hg inputs Strategies include (1) blocking key inorganic precursors... since bacteria are preferentially sorbed to the gas–water interface versus the solid–water interface ( Jewett et al., 1999 ; Powelson and Mills, 1996 , 1998 ; Schafer et al., 1998 ; Wan et al., 1994 )... Wallschlager et al., 1998 a,b), with adsorption increasing with increasing pH and decreasing with increased ligand complexation (e.g., Cl–) This is consistent with increasing evidence that Hg is
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