The Biogeochemistry of Submerged Soils

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<ul><li><p>The Biogeochemistryof Submerged Soils</p><p>The B iogeochemistry of Submerged Soils Guy Kirk 2004 John Wiley &amp; Sons, Ltd ISBN: 0-470-86301-3</p></li><li><p>The Biogeochemistryof Submerged Soils</p><p>Guy KirkNational Soil Resources InstituteCranfield University,UK and formerly International RiceResearch Institute, Philippines</p></li><li><p>Copyright 2004 John Wiley &amp; Sons Ltd, The Atrium, Southern Gate, Chichester,West Sussex PO19 8SQ, England</p><p>Telephone (+44) 1243 779777Email (for orders and customer service enquiries): our Home Page on or</p><p>All Rights Reserved. No part of this publication may be reproduced, stored in a retrieval system ortransmitted in any form or by any means, electronic, mechanical, photocopying, recording,scanning or otherwise, except under the terms of the Copyright, Designs and Patents Act 1988 orunder the terms of a licence issued by the Copyright Licensing Agency Ltd, 90 Tottenham CourtRoad, London W1T 4LP, UK, without the permission in writing of the Publisher. Requests to thePublisher should be addressed to the Permissions Department, John Wiley &amp; Sons Ltd, TheAtrium, Southern Gate, Chichester, West Sussex PO19 8SQ, England, or emailed, or faxed to (+44) 1243 770620.This publication is designed to provide accurate and authoritative information in regard to thesubject matter covered. It is sold on the understanding that the Publisher is not engaged inrendering professional services. If professional advice or other expert assistance is required, theservices of a competent professional should be sought.</p><p>Other Wiley Editorial Offices</p><p>John Wiley &amp; Sons Inc., 111 River Street, Hoboken, NJ 07030, USA</p><p>Jossey-Bass, 989 Market Street, San Francisco, CA 94103-1741, USA</p><p>Wiley-VCH Verlag GmbH, Boschstr. 12, D-69469 Weinheim, Germany</p><p>John Wiley &amp; Sons Australia Ltd, 33 Park Road, Milton, Queensland 4064, Australia</p><p>John Wiley &amp; Sons (Asia) Pte Ltd, 2 Clementi Loop #02-01, Jin Xing Distripark, Singapore 129809</p><p>John Wiley &amp; Sons Canada Ltd, 22 Worcester Road, Etobicoke, Ontario, Canada M9W 1L1</p><p>Wiley also publishes its books in a variety of electronic formats. Some content that appearsin print may not be available in electronic books.</p><p>Library of Congress Cataloging-in-Publication Data</p><p>Kirk, G. J. D.The biogeochemistry of submerged soils / Guy Kirk.</p><p>p. cm.Includes bibliographical references (p. ).</p><p>ISBN 0-470-86301-3 (cloth : alk. paper)1. Hydromorphic soils. 2. Soil chemistry. 3. Biogeochemistry. I.</p><p>Title.S592.17.H93K57 2004631.41dc22 2003019773</p><p>British Library Cataloguing in Publication Data</p><p>A catalogue record for this book is available from the British Library</p><p>ISBN 0-470-86301-3</p><p>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.</p></li><li><p>Contents</p><p>Preface ix</p><p>Acknowledgements xi</p><p>1 Introduction 11.1 Global Extent of Submerged Soils and Wetlands 11.2 Biogeochemical Characteristics 31.3 Types of Submerged Soil 9</p><p>1.3.1 Organic Soils 91.3.2 Mineral Soils 101.3.3 Relation between Soils and Landform 12</p><p>2 Transport Processes in Submerged Soils 172.1 Mass Flow 192.2 Diffusion 22</p><p>2.2.1 Diffusion Coefficients in Soil 222.2.2 Propagation of pH Changes Through Soil 35</p><p>2.3 Ebullition 382.4 Mixing by Soil Animals 39</p><p>3 Interchange of Solutes between Solid, Liquid and Gas Phases 45A. WATER 45</p><p>3.1 Composition of the Water 453.1.1 Acid and Bases 463.1.2 Speciation 473.1.3 Equilibrium Calculations 50</p><p>3.2 pH Buffer Capacity 533.3 Equilibrium with the Gas Phase 54</p><p>3.3.1 Floodwater CO2 Dynamics 563.4 Gas Transport Across the AirWater Interface 58</p><p>3.4.1 CO2 Transfer Across the AirWater Interface 61B. SOIL 65</p><p>3.5 The Solid Surfaces in Soils 653.6 The Solid Surfaces in Submerged Soils 69</p><p>3.6.1 Organic Matter in Submerged Soils 743.7 SolidSolution Interactions 76</p><p>3.7.1 Adsorption 76</p></li><li><p>vi Contents</p><p>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</p><p>4 Reduction and Oxidation 934.1 Thermodynamics and Kinetics of Redox Reactions 93</p><p>4.1.1 Electron Activities and Free Energy Changes 934.1.2 Redox Potentials 974.1.3 Relation between pe and Concentration of Redox</p><p>Couples 974.1.4 pepH Diagrams 994.1.5 Energetics of Reactions Mediated by Microbes 102</p><p>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</p><p>Reduction 1134.2.4 Measurement of Redox Potential in Soil 116</p><p>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</p><p>4.4 Oxidation of Reduced Soil 1274.4.1 Kinetics of Fe2+ Oxidation 1284.4.2 Simultaneous Diffusion and Oxidation in Soil 131</p><p>5 Biological Processes in the Soil and Floodwater 1355.1 Microbiological Processes 135</p><p>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</p><p>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</p><p>5.3 Is Biodiversity Important? 163</p></li><li><p>Contents vii</p><p>6 Processes in Roots and the Rhizosphere 1656.1 Effects of Anoxia and Anaerobicity on Plant Roots 165</p><p>6.1.1 Adaptations to Anoxia 1676.1.2 Armstrong and Becketts Model of Root Aeration 170</p><p>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</p><p>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</p><p>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</p><p>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</p><p>6.6 Conclusions 202</p><p>7 Nutrients, Toxins and Pollutants 2037.1 Nutrient and Acidity Balances 203</p><p>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</p><p>7.2 Toxins 2127.2.1 Acidity 2127.2.2 Iron Toxicity 2147.2.3 Organic Acids 2157.2.4 Salinity 216</p><p>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</p><p>8 Trace Gases 2338.1 Methane 233</p><p>8.1.1 Global Budget 2338.1.2 Processes Governing Methane Emissions from Rice 2348.1.3 Modelling Methane Emission 237</p></li><li><p>viii Contents</p><p>8.1.4 Estimating Emissions at the Regional Scale 2448.1.5 Possibilities For Decreasing Emissions 246</p><p>8.2 Nitrogen Oxides 2478.2.1 Global Budget 2478.2.2 Processes Governing Nitrous and Nitric Oxide</p><p>Emissions from Rice 2498.2.3 Differences between Rice Production Systems 250</p><p>8.3 Ammonia 2528.3.1 Global Budget 2528.3.2 Processes Governing Ammonia Emissions from Rice 254</p><p>8.4 Sulfur Compounds 2568.4.1 Global Budget 2568.4.2 Emissions from Ricefields 256</p><p>8.5 Carbon Sequestration 258</p><p>References 259</p><p>Index 283</p></li><li><p>Preface</p><p>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.</p><p>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.</p><p>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 research has been done on these topics for submergedsoils than for dryland soils, in spite of their importance. But knowledge and under-standing of them have increased substantially in the past few decades. Much ofthe research has been on rice soils, particularly at the International Rice ResearchInstitute (IRRI) which has been involved in research on submerged soils since itwas founded in 1960. But there is also much in the ecological and environmentalliteratures concerned with natural wetlands. In preparing the book I have aimedto deal with generic principles relevant to both natural and artificial wetlandswith the aim of serving audiences for both.</p></li><li><p>Acknowledgements</p><p>I thank the following friends and colleagues for their help in planning the bookand reviewing draft chapters: Dave Bouldin, Roland Buresh, Ralph Conrad,Achim Dobermann, Dennis Greenland, Peter Nye, Bill Patrick, John Sheehy,Siobhan Staunton, Dick Webster and Oswald van Cleemput. I am indebted to theDirector General of IRRI, Ron Cantrell, for the award of a consultancy to writethe book and for his encouragement throughout. Most of the writing was doneduring a sabbatical in the Department of Plant Sciences, University of Cambridge,and I am grateful to the Head of Department, Roger Leigh, and member of theDepartment for their hospitality. The book was completed during my first monthsat the National Soil Resources Institute, Cranfield University, and I am indebtedto the Director, Mark Kibblewhite, for his encouragement and forbearance. Forhelp with the artwork I am grateful to Edwin Javier, Ely Tabaquero and GeneHettel, all of IRRI.</p></li><li><p>1 Introduction</p><p>Submerged soils behave and affect the environment in substantially different waysto dryland soils. This chapter discusses the main characteristics and environmentaleffects of submerged soils and the wetlands they support, and their extent acrossthe globe.</p><p>1.1 GLOBAL EXTENT OF SUBMERGED SOILS AND WETLANDS</p><p>For the purposes of the book I define wetlands as lands that are intermittentlyor permanently inundated with water to a depth of no more than a few metres.Depending on the precise definition applied, estimates of the total global wetlandarea range from 700 to 1000 Mha (Aselmann and Crutzen, 1989; Scharpenseel,1997; Mitsch and Gosselink, 2000). Figure 1.1 shows their approximate distri-bution and Table 1.1 the extents of different types distinguished by hydrology,vegetation and soil characteristics. The largest areas are the bogs and fens inpolar and boreal regions in North America and Russia (34 % of total area); trop-ical swamps, especially in East Africa and South America (14 % of total area);tropical floodplains, especially of the Amazon and the rivers of South East Asia(10 %); and temperate and tropical ricefields (4 and 12 %, respectively). Almosthalf the global wetland area is in the tropics. There has been considerable lossof wetlands in many parts of the world over the past 200 years as a result ofconversion to agricultural and aquacultural uses. In the US for example, it isestimated that the area has declined from 89 Mha in the 1780s to 49 Mha in the1980s (Mitsch and Gosselink, 2000).</p><p>A special class of wetland is the lowland ricefield, which accounts for almost afifth of the wetland area worldwide. Much of our knowledge and understandingof submerged soils has been gained from research on rice soils. The successof rice as a food crop stems from its origins as a wetland plant and its abilityto withstand soil submergence with the attendant improvements in water andnutrient supplies. A corollary is that rice is more sensitive to water deficiencythan most other crops, and the critical factors in its productivity are the supplyof water to the soil, from rain, river, reservoir or groundwater, and the abilityof the soil to retain water. Hence most rice is produced and the highest yieldsattained on the alluvial deposits associated with major rivers and their deltas.More than 90 % of the production is in Asia, distributed unevenly over four rice</p><p>The B iogeochemistry of Submerged Soils Guy Kirk 2004 John Wiley &amp; Sons, Ltd ISBN: 0-470-86301-3</p></li><li><p>2 Introduction</p><p>40</p><p>20</p><p>0</p><p>20</p><p>40</p><p>160 140 120 100 80 60 40 20 0 20 40 60 80 100 120 140 160</p><p>Equator</p><p>Major Wetland Area</p><p>Area with AbundantWetlands</p><p>Figure 1.1 Global distribution of wetlands (Mitsch and Gosselink, 2000). Reproducedby permission of Wiley, New York</p><p>Table 1.1 Global extent of wetlands of different types</p><p>Area (Mha)</p><p>Polar Boreal Temperate Tropical Total</p><p>Bogs 21 104 42 20 187Fens 54 62 32 148Swamps 1 10 102 113Marshes 17 10 27Floodplains 8 74 82Shallow lakes 1 11 12Ricefields 29 80 109Total 75 167 139 297 678</p><p>Definitions of wetland types:Bogs are raised peat-producing wetlands formed in wet climates where organic material has accumulated overlong periods. Because they are raised, water and nutrients are entirely derived from the atmosphere, and they aretherefore nutrient deficient and acid. Sphagnum moss is the main vegetation, though other types of vegetation arealso present in tropical regions.Fens are peat-producing wetlands that receive water and nutrients through inflow from neighbouring land. Theyare generally less acid than bogs and may be alkaline, and tend to be dominated by grasses and sedges. Becauseof their better nutrient status they are generally more prolific than bogs.Swamps are forested, freshwater wetlands on submerged soils in which little peat accumulates. This is the USdefinition; elsewhere the term also includes non-forested wetlands with reeds. Swamps tend to form in warmerclimates.Marshes are herba...</p></li></ul>


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