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<ul><li><p>Methods in Biogeochemistry of Wetlands</p><p>R.D. DeLaune, K.R. Reddy, C.J. Richardson, and J.P. Megonigal, editors</p><p>Book and Multimedia Publishing CommitteeApril Ulery, ChairWarren Dick, ASA Editor-in-ChiefE. Charles Brummer, CSSA Editor-in-ChiefAndrew Sharpley, SSSA Editor-in-ChiefLajpat Ahuja Michael Casler David Clay Kimberly Cook David Fang Girisha GanjegunteRobert Graham Zhongqi He Srirama Krishna Reddy Shuyu Liu Sally Logsdon Thomas Mueller Mary Savin Nooreldeen Shawqi Ali Gurpal Toor Director of Publications: Mark MandelbaumManaging Editor: Lisa Al-AmoodiBooks Acquisitions Editor: Nicole Sandler</p><p>Number 10 in the Soil Science Society of America Book SeriesSally Logsdon, series editorPublished by Soil Science Society of America, Inc., Madison, Wisconsin, USA</p></li><li><p>Copyright 2013 by Soil Science Society of America</p><p>ALL RIGHTS RESERVED. No part of this publication may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, recording, or any information storage and retrieval system, without permission in writing from the publisher. </p><p>The views expressed in this publication represent those of the individual Editors and Authors. These views do not necessarily reflect endorsement by the Publisher(s). In addition, trade names are sometimes mentioned in this publication. No endorsement of these products by the Publisher(s) is intended, nor is any criticism implied of similar products not mentioned.</p><p>Soil Science Society of America, Inc.5585 Guilford Road, Madison, WI 53711-5801 USA</p><p></p><p>ISBN: 978-0-89118-960-2 (print) ISBN: 978-0-89118-961-9 (electronic)doi:10.2136/sssabookser10Library of Congress Control Number: 2013951552</p><p>SSSA Book Series ISSN: 2163-2804 (online)ISSN: 1047-4986 (print)</p><p>Cover design: Patricia ScullionCover photo: A small stand of pond cypress [Taxodium distichum (L.) Rich.] displaying their fall colors prior to leaf drop on the shore of a dystrophic Carolina Bay Lake Wetland complex in Jones Lake State Park in Bladen county, NC. Photograph by Dr. Curtis J. Richardson, Director of the Duke University Wetland Center, Durham, NC. </p><p>Printed in the United States of America.</p></li><li><p>v</p><p>ContentsForeword xiiPreface xiiiContributors xv</p><p>Chapter 1Issues of Sampling Design in Wetlands 1</p><p>Monica Rivas Casado, Ron Corstanje, Pat Bellamy, and Ben MarchantDESIGN-BASED SAMPLING APPROACHES 8MODEL-BASED SAMPLING APPROACHES 11</p><p>Chapter 2Soil and Sediment Sampling of Inundated Environments 21</p><p>Todd Z. Osborne and R.D. DeLauneSAMPLING IN INUNDATED ENVIRONMENTS: SAMPLING PLAN AND GENERAL CONSIDERATIONS 22SAMPLING METHODS FOR INUNDATION DEPTHS LESS THAN 1.5 METERS 26SAMPLING METHODS FOR INUNDATION DEPTHS GREATER THAN 1.5 METERS 32SPECIAL CONDITIONS OR CONSIDERATIONS 36</p><p>Chapter 3Physicochemical Characterization of Wetland Soils 41</p><p>K.R. Reddy, M.W. Clark, R.D. DeLaune, and M. KongchumSOIL SAMPLING 42PHYSICOCHEMICAL PROPERTIES 43CONCLUSIONS 52</p><p>Chapter 4Soil Pore Water Sampling Methods 55</p><p>M.M. Fisher and K.R. ReddyTECHNIQUES FOR SAMPLING SOIL PORE WATER 56SAMPLE HANDLING CONSIDERATIONS 64SAMPLING PORE WATER GASES 66SUMMARY 68</p><p>Chapter 5ReductionOxidation Potential and Oxygen 71</p><p>J. Patrick Megonigal and Martin RabenhorstREDOX POTENTIAL THEORY 73OXYGEN MEASUREMENT WITH DIFFUSION CHAMBERS 73REDOX MEASUREMENT 78</p><p>Chapter 6Determination of Dissolved Oxygen, Hydrogen Sulfide, Iron(II), and Manganese(II) in Wetland Pore Waters 87</p><p>George W. Luther III and Andrew S. MadisonEXPERIMENTAL PRINCIPLES OF ELECTRODE FABRICATION 91EXPERIMENTAL PRINCIPLES OF WORKING ELECTRODE CALIBRATIONS 96PROCEDURES FOR MICROPROFILING 101SUMMARY 104</p><p>Chapter 7Soil Redox Potential and pH Controllers 107</p><p>Kewei Yu and Jrg RinklebeREDOX POTENTIAL AND pH CONTROL 108MODIFICATIONS 110AN AUTOMATED BIOGEOCHEMICAL MICROCOSM SYSTEM 112APPLICATIONS 114</p></li><li><p>vi</p><p>Chapter 8Morphological Methods to Characterize Hydric Soils 117</p><p>M.J. VepraskasEQUIPMENT 120METHODS AND TECHNIQUES FOR DESCRIBING HYDRIC SOILS 122FIELD TEST TO ASSESS SOIL MATERIAL TYPE 124IDENTIFYING HYDRIC SOIL FIELD INDICATORS 132</p><p>Chapter 9Emergent Macrophyte Biomass Production 137</p><p>Christopher CraftSAMPLING CONSIDERATIONS 139INDIRECT METHODS 139DIRECT METHODS 144EMERGING METHODS 151</p><p>Chapter 10Photosynthetic Measurements in Wetlands 155</p><p>S.R. PezeshkiOXYGEN EXCHANGE MEASUREMENT TECHNIQUE 157CARBON ISOTOPE TECHNIQUE 158MICROMETEOROLOGICAL TECHNIQUE 159CHLOROPHYLL FLUORESCENCE METHOD 161PHOTOSYNTHETIC MEASUREMENTS USING CHAMBERS 165SUMMARY 173</p><p>Chapter 11Gas Transport and Exchange through Wetland Plant Aerenchyma 177</p><p>Brian K. Sorrell and Hans BrixGENERAL PRINCIPLES 178EXPERIMENTAL PRINCIPLES 180LABORATORY AND GLASSHOUSE CHAMBERS 184MODELING APPROACHES 190</p><p>Chapter 12A Primer on Sampling Plant Communities in Wetlands 197</p><p>Curtis J. Richardson and Ryan S. KingOVERVIEW OF SAMPLING PLANT POPULATIONS AND COMMUNITIES 199SAMPLE SIZE 200PLANT SAMPLING APPROACHES 203RAPID ASSESSMENT APPROACHES TO ESTIMATE PLANT ABUNDANCE AND COVER PERCENTAGE 206PLANT SAMPLING METHODS AND CALCULATION PROCEDURES 207ANALYSIS OF DATA 211COMPARISON OF PLANT COMMUNITIES 212SUGGESTIONS FOR DEVELOPING A PLANT SAMPLING PROGRAM 215APPENDIX 218</p><p>Chapter 13Plant ProductivityBottomland Hardwood Forests 225</p><p>William H. Conner and Julia A. CherryABOVEGROUND PRODUCTIVITY 228BELOWGROUND PRODUCTIVITY 234</p><p>Chapter 14 Current Methods to Evaluate Net Primary Production and Carbon Budgets in Mangrove Forests 243</p><p>Victor H. Rivera-Monroy, Edward Castaeda-Moya, Jordan G. Barr, Vic Engel, Jose D. Fuentes, Tiffany G. Troxler, Robert R. Twilley, Steven Bouillon, Thomas J. Smith III, and Thomas L. OHalloran</p><p>CURRENT METHODS TO ESTIMATE NET PRIMARY PRODUCTIVITY 245COMPARING MANGROVE NET PRIMARY PRODUCTION ESTIMATES TO WHOLE-FOREST CARBON FLUX MEASUREMENTS 263SUMMARY AND FUTURE RESEARCH DIRECTIONS 275APPENDIX 276</p></li><li><p>vii contents</p><p>Chapter 15Characterization of Wetland Soil Organic Matter 289</p><p>Robert L. Cook and Thomas S. BianchiSAMPLE TREATMENT AND PROCESSING 290SPECTROSCOPIC CHARACTERIZATION 292BULK ELEMENTAL AND CHEMICAL BIOMARKER ANALYSES 301SUMMARY 309</p><p>Chapter 16Dissolved Organic Matter 317</p><p>Robert G. QuallsEQUIPMENT AND INSTRUMENTATION 321MATERIALS AND REAGENTS 321SAMPLE PREPARATION 323PROCEDURES 323CONCLUSIONS 327</p><p>Chapter 17Soil Microbial Biomass and Phospholipid Fatty Acids 331</p><p>Jrg Rinklebe and Uwe LangerTHE SUBSTRATE-INDUCED RESPIRATION METHOD 333PHOSPHOLIPID FATTY ACIDS 338ESTIMATES OF MICROBIAL BIOMASS 343SUMMARY 343</p><p>Chapter 18Molecular Genetic Analysis of Wetland Soils 349</p><p>Hee-Sung Bae and Andrew V. OgramDNA EXTRACTION 350QUANTITATIVE POLYMERASE CHAIN REACTION 354POLYMERASE CHAIN REACTION BASED MOLECULAR CLONING 362</p><p>Chapter 19Enzyme Activities 373</p><p>Hojeong Kang, Seon-Young Kim, and Chris FreemanEQUIPMENT AND INSTRUMENTATION 376MATERIALS AND REAGENTS 376SAMPLE PREPARATION 377PROCEDURE 377CALCULATION 377SUMMARY 378</p><p>Chapter 20Organic Matter Mineralization and Decomposition 385</p><p>Scott D. Bridgham and Rongzhong YeLITTER DECOMPOSITION 386DECOMPOSITION OF STANDARD SUBSTRATES 393SOIL HETEROTROPHIC RESPIRATION 393PHOTODEGRADATION 403</p><p>Chapter 21Methanogenesis and Methane Oxidation in Wetland Soils 407</p><p>Kanika S. Inglett, Jeffery P. Chanton, and Patrick W. InglettEXPERIMENTAL METHANE MEASUREMENTS 409ISOTOPIC MEASUREMENTS OF METHANE 417</p><p>Chapter 22Greenhouse Gas Emission by Static Chamber and Eddy Flux Methods 427</p><p>Kewei Yu, April Hiscox, and R.D. DeLauneSTATIC CHAMBER MEASUREMENT 428EDDY COVARIANCE MEASUREMENT 432SUMMARY 436</p></li><li><p>viii</p><p>Chapter 23Characterization of Organic Nitrogen in Wetlands 439</p><p>C.M. VanZomeren, H. Knicker, W.T. Cooper, and K.R. ReddyCHEMICAL FRACTIONATION OF SOIL ORGANIC NITROGEN 440CHLOROFORM FUMIGATION METHOD 446NUCLEAR RESONANCE SPECTROSCOPY 448MASS SPECTROMETRY OF ORGANIC NITROGEN 454CONCLUSIONS 458</p><p>Chapter 24Measurements of Nitrogen Mineralization Potential in Wetland Soils 465</p><p>Eric D. Roy and John R. WhitePOTENTIALLY MINERALIZABLE NITROGEN 467SUBSTRATE-INDUCED NITROGEN MINERALIZATION 469LIMITATIONS 470SUMMARY 471</p><p>Chapter 25Wind Tunnel Method for Measurement of Ammonia Volatilization 473</p><p>M.E. Poach, K.S. Ro, and P.G. HuntEQUIPMENT AND INSTRUMENTATION 476MATERIALS AND REAGENTS 479SAMPLE PREPARATION 479PROCEDURE 480SAMPLE ANALYSIS 480CALCULATION 481STATISTICAL ANALYSIS 481QUALITY ASSURANCE 481SUMMARY 482</p><p>Chapter 26Ammonium Oxidation in Wetland Soils 485</p><p>K.S. Inglett, A.V. Ogram, and K.R. ReddyAEROBIC AMMONIUM OXIDATION (NITRIFICATION) 486ANAEROBIC AMMONIUM OXIDATION (ANAMMOX) 488METHODS FOR ASSESSING AEROBIC AMMONIUM OXIDATION (NITRIFICATION) 489METHODS FOR ASSESSING ANAEROBIC AMMONIUM OXIDATION (ANAMMOX) POTENTIAL 492MOLECULAR METHODS FOR ASSESSING AMMONIUM OXDIATION IN WETLAND SOILS 494SUMMARY 497</p><p>Chapter 27Denitrification Measurement Using Membrane Inlet Mass Spectrometry 503</p><p>Patrick W. Inglett, Todd M. Kana, and Soonmo AnGENERAL PRINCIPLES 504EXPERIMENTAL PRINCIPLES 505ISOTOPE PAIRING BY THE MIMS METHOD 510SUMMARY 516</p><p>Chapter 28Nitrate Reduction, Denitrification, and Dissimilatory Nitrate Reduction to Ammonium in Wetland Sediments 519</p><p>Amy J. Burgin, Stephen K. Hamilton, Wayne S. Gardner, and Mark J. McCarthyEQUIPMENT AND INSTRUMENTATION 521MATERIALS AND REAGENTS 524PROCEDURES 525SAMPLE PREPARATION 530CALCULATIONS 533</p><p>Chapter 29System-Level Denitrification Measurement Based on Dissolved Gas Equilibration Theory and Membrane Inlet Mass Spectrometry 539</p><p>Andrew Laursen and Patrick W. InglettGENERAL THEORY 541EXPERIMENTAL PRINCIPLES 541CALCULATIONS 544DISCUSSION AND LIMITATIONS 549SUMMARY 550</p></li><li><p>ix contents</p><p>Chapter 30Biogeochemical Nitrogen Cycling in Wetland Ecosystems: Nitrogen-15 Isotope Techniques 553</p><p>Dries Huygens, Mark Trimmer, Tobias Rtting, Christoph Mller, Catherine M. Heppell, Katrina Lansdown, and Pascal Boeckx</p><p>EXPERIMENTAL STUDY SETUPS 554ISOTOPE PAIRING AND REVISED ISOTOPE PAIRING TECHNIQUES 555ISOTOPE DILUTION AND TRACING TECHNIQUES 573</p><p>Chapter 31Biological Dinitrogen Fixation 593</p><p>Patrick W. InglettACETYLENE REDUCTION 594DINITROGEN-15 INCORPORATION 598SUMMARY 601</p><p>Chapter 32Methods for Soil Phosphorus Characterization and Analysis of Wetland Soils 603</p><p>Curtis J. Richardson and K.R. ReddyTERMINOLOGY, OPERATIONAL DEFINITIONS, AND COMPARISON OF PHOSPHORUS FORMS 607SAMPLE PREPARATION AND STORAGE 609SOIL PHOSPHORUS ANALYSIS 610PHOSPHORUS AVAILABILITY INDICES 618ANION EXCHANGE RESIN AND IRON OXIDE PAPER 625SOIL INORGANIC PHOSPHORUS FORMS 626GENERAL COMMENTS 631</p><p>Chapter 33Phosphorus Characterization in Wetland Soils by Solution Phosphorus-31 Nuclear Magnetic Resonance Spectroscopy 639</p><p>Alexander W. Cheesman, James Rocca, and Benjamin L. TurnerBRIEF OVERVIEW OF THE PRINCIPLES 641APPLICATION TO WETLAND SOILS 647</p><p>Chapter 34Phosphorus Sorption and Desorption in Wetland Soils 667</p><p>Vimala D. Nair and K. Ramesh ReddyBATCH INCUBATION TECHNIQUE 669CALCULATIONS 670THE SINGLE-POINT ISOTHERM 673APPLICATIONS OF PHOSPHORUS SORPTION INDICES 674SUMMARY 678</p><p>Chapter 35Organic Phosphorus Mineralization in Wetland Soils 683</p><p>K.R. Reddy, T. Chua, and Curtis J. RichardsonORGANIC PHOSPHORUS POOLS 684ENZYMATIC HYDROLYSIS OF ORGANIC PHOSPHORUS 689POTENTIALLY MINERALIZABLE PHOSPHORUS 690CONCLUSIONS 696</p><p>Chapter 36Iron and Manganese ReductionOxidation 701</p><p>Martin Pentrk, Linda Pentrkov, and Joseph W. StuckiSAMPLING 702INERT-ATMOSPHERE SAMPLE HANDLING 703IRON 706MANGANESE 708SAMPLE PREPARATION FOR FURTHER ANALYSES 711SUMMARY 715</p></li><li><p>x</p><p>Chapter 37Using Synthesized Iron Oxides as an Indicator of Reduction in Soils 723</p><p>M.C. RabenhorstEQUIPMENT AND INSTALLATION 725MATERIALS AND REAGENTS 725PROCEDURES 729CONCLUSIONS 738</p><p>Chapter 38Characterization of Sulfur Forms and Isotopic Compositions in Wetland Soils 741</p><p>William H. Orem and Anne L. BatesANALYSIS OF TOTAL SULFUR IN WETLAND SOIL 743SPECIATION OF SULFUR IN WETLAND SOIL 748SULFUR ISOTOPE ANALYSIS 760</p><p>Chapter 39Measurement of Sulfate Reduction in Wetland Soils 765</p><p>Jeffrey C. CornwellEQUIPMENT 768MATERIALS AND REAGENTS 769CORE COLLECTION AND INCUBATION 770SAMPLE DIGESTION 771CALCULATION 772RADIATION AND CHEMICAL SAFETY 772</p><p>Chapter 40Total Heavy Metal Analyses and Extractions 775</p><p>Robert P. GambrellIMPORTANCE OF METALS 776METAL LEVELS IN UPLAND VS. WETLAND SOILS AND SEDIMENTS 777FORMS OF METALS IN SOILS, WETLAND SOILS, AND SEDIMENTS 779PRECAUTIONS AND PROCEDURES FOR ANAEROBIC SAMPLES 783PROCESSING WATER SAMPLES FOR METALS 785SOIL AND SEDIMENT SAMPLES 790WETLAND SOIL AND SEDIMENT EXTRACTIONS 793INSTRUMENTAL ANALYSES 796QUALITY CONTROL 796</p><p>Chapter 41Speciation of Arsenic(III)/Arsenic(V) and Selenium(IV)/Selenium(VI) Using Coupled Ion ChromatographyHydride Generation Atomic Absorption Spectrometry 801</p><p>Sabine Goldberg and Bruce A. ManningEQUIPMENT AND INSTRUMENTATION 804REAGENTS AND MATERIALS 804SAMPLE PREPARATION 808PROCEDURE 809RESULTS 809CONCLUSIONS 812</p><p>Chapter 42Methods for Determining Toxic Organic Compounds in Wetlands 815</p><p>Elisa DAngeloSAMPLING AND PRESERVATION 816EXTRACTION 823EXTRACT CLEANUP 827DETERMINATIVE METHODS 829CALIBRATION CALCULATIONS 832SUMMARY 835</p></li><li><p>xi contents</p><p>Chapter 43Methods for Determining Emerging Contaminants in Wetland Matrices 841</p><p>Jeremy L. Conkle, John R. White, and Chris D. MetcalfeGENERAL METHOD INFORMATION 843QUALITY ASSURANCE/QUALITY CONTROL 844SAMPLE COLLECTION, STORAGE, AND HOLD TIMES 844SAMPLE PREPARATION 845EXTRACTION, CONCENTRATION, AND SOLID EXTRACT CLEANUP 849ANALYTICAL METHODS 850CALCULATIONS 851METHOD APPLICATION AND ADAPTATIONS 852SUMMARY 853</p><p>Chapter 44Nanoscale Analytical Transmission Electron Microscopy Techniques Applicable to Wetland Research and Monitoring 857</p><p>Bojeong Kim, Curtis J. Richardson, Mitsuhiro Murayama, and Michael F. Hochella, Jr.MODERN ANALYTICAL TRANSMISSION ELECTRON MICROSCOPY: A SYNOPSIS 859SAMPLE PREPARATION 861TRANSMISSION ELECTRON MICROSCOPY ANALYSES 863</p><p>Chapter 45Dating Wetland Sediment Cores 879</p><p>Mark Brenner and William F. KenneyRADIOCARBON DATING 880LEAD-210 DATING 885SUMMARY 898</p><p>Chapter 46The Surface Elevation TableMarker Horizon Method for Measuring Wetland Accretion and Elevation Dynamics 901</p><p>John C. Callaway, Donald R. Cahoon, and James C. LynchPREVIOUS USES 904EQUIPMENT AND INSTRUMENTATION 905MATERIALS AND REAGENTS 908PROCEDURE 909CALCULATIONS 913</p><p>Chapter 47Wetland Water Budgets 919</p><p>Jennifer Mitchell and James W. JawitzWATER BUDGET 920DATA REQUIRED 922EXAMPLE WATER BUDGETS 926SUMMARY OF WATER BUDGET APPLICATIONS 933</p><p>Chapter 48On the Calculation of the Flux of Materials through Wetlands and Estuaries under Oscillatory Motions 937</p><p>Chunyan Li, John R. White, and Sibel BarguMETHOD 939APPLICATION AND DISCUSSION 941SUMMARY 946</p><p>Chapter 49Methods to Assess High-Resolution Subsurface Gas Concentrations and Gas Fluxes in Wetland Ecosystems 949</p><p>Bo Elberling, Michael Khl, Ronnie N. Glud, Christian Juncher Jrgensen, Louise Askaer, Lars F. Rickelt, Hans P. Joensen, Morten Larsen, and Lars Liengaard</p><p>SUBSURFACE GAS MEASUREMENTS 950NET SURFACE GAS FLUX MEASUREMENTS 963CONCLUSIONS 966</p><p>Index 971</p></li><li><p>xii</p><p>Foreword</p><p>Wetlands only occupy 6% of the Earths surface, yet their role in the eco-sphere is much greater than their extent suggests....</p></li></ul>