the biogeochemistry of submerged soils

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  • The Biogeochemistryof Submerged Soils

    The B iogeochemistry of Submerged Soils Guy Kirk 2004 John Wiley & Sons, Ltd ISBN: 0-470-86301-3

  • The Biogeochemistryof Submerged Soils

    Guy KirkNational Soil Resources InstituteCranfield University,UK and formerly International RiceResearch Institute, Philippines

  • Copyright 2004 John Wiley & Sons Ltd, The Atrium, Southern Gate, Chichester,West Sussex PO19 8SQ, England

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    Library of Congress Cataloging-in-Publication Data

    Kirk, G. J. D.The biogeochemistry of submerged soils / Guy Kirk.

    p. cm.Includes bibliographical references (p. ).

    ISBN 0-470-86301-3 (cloth : alk. paper)1. Hydromorphic soils. 2. Soil chemistry. 3. Biogeochemistry. I.

    Title.S592.17.H93K57 2004631.41dc22 2003019773

    British Library Cataloguing in Publication Data

    A catalogue record for this book is available from the British Library

    ISBN 0-470-86301-3

    Typeset in 10/12pt Times by Laserwords Private Limited, Chennai, IndiaPrinted and bound in Great Britain by Antony Rowe Ltd, Chippenham, WiltshireThis book is printed on acid-free paper responsibly manufactured from sustainable forestryin which at least two trees are planted for each one used for paper production.

  • Contents

    Preface ix

    Acknowledgements xi

    1 Introduction 11.1 Global Extent of Submerged Soils and Wetlands 11.2 Biogeochemical Characteristics 31.3 Types of Submerged Soil 9

    1.3.1 Organic Soils 91.3.2 Mineral Soils 101.3.3 Relation between Soils and Landform 12

    2 Transport Processes in Submerged Soils 172.1 Mass Flow 192.2 Diffusion 22

    2.2.1 Diffusion Coefficients in Soil 222.2.2 Propagation of pH Changes Through Soil 35

    2.3 Ebullition 382.4 Mixing by Soil Animals 39

    3 Interchange of Solutes between Solid, Liquid and Gas Phases 45A. WATER 45

    3.1 Composition of the Water 453.1.1 Acid and Bases 463.1.2 Speciation 473.1.3 Equilibrium Calculations 50

    3.2 pH Buffer Capacity 533.3 Equilibrium with the Gas Phase 54

    3.3.1 Floodwater CO2 Dynamics 563.4 Gas Transport Across the AirWater Interface 58

    3.4.1 CO2 Transfer Across the AirWater Interface 61B. SOIL 65

    3.5 The Solid Surfaces in Soils 653.6 The Solid Surfaces in Submerged Soils 69

    3.6.1 Organic Matter in Submerged Soils 743.7 SolidSolution Interactions 76

    3.7.1 Adsorption 76

  • vi Contents

    3.7.2 Precipitation 793.7.3 Co-Precipitation in Solid Solutions 823.7.4 Inhibition of Precipitation 853.7.5 Equations for SolidSolution Interactions 87

    4 Reduction and Oxidation 934.1 Thermodynamics and Kinetics of Redox Reactions 93

    4.1.1 Electron Activities and Free Energy Changes 934.1.2 Redox Potentials 974.1.3 Relation between pe and Concentration of Redox

    Couples 974.1.4 pepH Diagrams 994.1.5 Energetics of Reactions Mediated by Microbes 102

    4.2 Redox Conditions in Soils 1064.2.1 Changes with Depth in the Soil 1074.2.2 Changes with Time 1094.2.3 Calculated Changes in pe, pH and Fe During Soil

    Reduction 1134.2.4 Measurement of Redox Potential in Soil 116

    4.3 Transformations of Nutrient Elements AccompanyingChanges in Redox 1194.3.1 Transformations of Carbon 1204.3.2 Transformations of Nitrogen 1204.3.3 Transformations of Sulfur 1224.3.4 Transformations of Phosphorus 124

    4.4 Oxidation of Reduced Soil 1274.4.1 Kinetics of Fe2+ Oxidation 1284.4.2 Simultaneous Diffusion and Oxidation in Soil 131

    5 Biological Processes in the Soil and Floodwater 1355.1 Microbiological Processes 135

    5.1.1 Processes Involved in Sequential Reduction 1365.1.2 Nitrate Reduction 1415.1.3 Iron and Manganese Reduction 1425.1.4 Sulfate Reduction 1435.1.5 Methanogenesis 1445.1.6 Aerobic Processes 147

    5.2 Macrobiological Processes 1505.2.1 Net Primary Production and Decomposition 1505.2.2 The FloodwaterSoil System 1515.2.3 Floodwater Properties 1525.2.4 Floodwater Flora 1545.2.5 Fauna 159

    5.3 Is Biodiversity Important? 163

  • Contents vii

    6 Processes in Roots and the Rhizosphere 1656.1 Effects of Anoxia and Anaerobicity on Plant Roots 165

    6.1.1 Adaptations to Anoxia 1676.1.2 Armstrong and Becketts Model of Root Aeration 170

    6.2 Architecture of Wetland Plant Root Systems 1716.2.1 Model of Root Aeration versus Nutrient Absorption 1726.2.2 Root Surface Required for Nutrient Absorption 177

    6.3 Nutrient Absorption Properties of Wetland Plant Roots 1806.3.1 Ion Transport in Roots 1806.3.2 Ion Transport in Wetland Roots 184

    6.4 Root-Induced Changes in the Soil 1906.4.1 Oxygenation of the Rhizosphere 1916.4.2 The pH Profile Across the Rhizosphere 194

    6.5 Consequences of Root-induced Changes 1966.5.1 NitrificationDenitrification in the Rhizosphere 1966.5.2 Solubilization of Phosphate 1976.5.3 Solubilization of Zinc 2006.5.4 Immobilization of Cations 200

    6.6 Conclusions 202

    7 Nutrients, Toxins and Pollutants 2037.1 Nutrient and Acidity Balances 203

    7.1.1 Nutrient Balances in Ricefields 2037.1.2 Acidity Balances in Ricefields 2087.1.3 Peat Bogs 2107.1.4 Riparian Wetlands 2107.1.5 Tidal Wetlands 211

    7.2 Toxins 2127.2.1 Acidity 2127.2.2 Iron Toxicity 2147.2.3 Organic Acids 2157.2.4 Salinity 216

    7.3 Trace Elements 2187.3.1 Global Cycling of Trace Elements 2187.3.2 Transport Through Soil and into Plant Roots 2187.3.1 Mobilities of Individual Trace Elements 220

    8 Trace Gases 2338.1 Methane 233

    8.1.1 Global Budget 2338.1.2 Processes Governing Methane Emissions from Rice 2348.1.3 Modelling Methane Emission 237

  • viii Contents

    8.1.4 Estimating Emissions at the Regional Scale 2448.1.5 Possibilities For Decreasing Emissions 246

    8.2 Nitrogen Oxides 2478.2.1 Global Budget 2478.2.2 Processes Governing Nitrous and Nitric Oxide

    Emissions from Rice 2498.2.3 Differences between Rice Production Systems 250

    8.3 Ammonia 2528.3.1 Global Budget 2528.3.2 Processes Governing Ammonia Emissions from Rice 254

    8.4 Sulfur Compounds 2568.4.1 Global Budget 2568.4.2 Emissions from Ricefields 256

    8.5 Carbon Sequestration 258

    References 259

    Index 283

  • Preface

    This book is about the movements and transformations of energy and matter insoils that are continuously or intermittently submerged with water. Submergedsoils cover a huge area, from 5 to 7 per cent of the Earths land surface, and theyare undoubtedly of great practical importance: in local, regional and global ele-ment cycles, as habitats for plants and wildlife, and in food and fibre production.The submerged soils in ricefields, for example, produce the basic food of morethan 2 billion people, a third of the world population. But submerged soils arealso inherently interesting scientifically, and that is the main theme of the book.

    When a soil is submerged, air is excluded and the soil quickly becomes anoxic.A submerged soil is therefore an open, anoxic chemical system, surrounded byoxic systems with very different characteristics. Energy enters through photosyn-thesis, and inorganic matter enters with percolating water and by gas exchange.Chemical reactions occur through a complicated interchange between solid, liq-uid and gas phases, largely mediated by biological processes. Further, becauseplants are the main conduits for gas exchange between the soil and overlyingatmosphere, they have a particularly important influence. Submerged soils there-fore provide a unique natural laboratory for studying a great range of physical,chemical and biological processes that are important in environmental systems.They form under a wide range of hydrological, geological and topographicalconditions, but because of the overriding influence of anoxia, the soils and plantsand microbes adapted to them have various characteristics in common.

    The book describes the physical, chemical and biological processes operatingin submerged soils and links them to the dynamics of nutrients, toxins, pollutantsand trace gases. Far less res


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