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Biofilms in Bioelectrochemical Systems BIOFILMS IN BIOELECTROCHEMICAL SYSTEMS BIOFILMS IN BIOELECTROCHEMICAL SYSTEMS From Laboratory Practice to Data Interpretation HALUK BEYENAL JEROME T. BABAUTA Copyright © 2015 by John Wiley & Sons, Inc. All rights reserved Published by John Wiley & Sons, Inc., Hoboken, New Jersey Published simultaneously in Canada MATLAB and Simulink are registered trademarks of The MathWorks, Inc. See www.mathworks.com/trademarks for a list of additional trademarks. The MathWorks Publisher Logo identifies books that contain MATLAB® content. Used with permission. The MathWorks does not warrant the accuracy of the text or exercises in this book or in the software downloadable from http://www.wiley.com/WileyCDA/WileyTitle/productCd-047064477X.html and http://www.mathworks.com/matlabcentral/fileexchange/?term=authorid%3A80973. 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This book’s use or discussion of MATLAB® software or related products does not constitute endorsement or sponsorship by The MathWorks of a particular pedagogical approach or particular use of the MATLAB® software. Library of Congress Cataloging-in-Publication Data: Beyenal, H. Biofilms in bioelectrochemical systems : from laboratory practice to data interpretation / Haluk Beyenal, Jerome T. Babauta. pages cm Includes index. ISBN 978-1-118-41349-4 (hardback) 1. Fuel cells–Materials. 2. Energy harvesting. 3. Biofilms–Industrial applications. 4. Bioelectrochemistry–Industrial applications. I. Babauta, Jerome T. II. Title. TK2931.B488 2015 621.31′24290284–dc23 2015010200 Typeset in 10/12pt, TimesLtStd by SPi Global, Chennai, India Printed in the United States of America 10987654321 1 2015 CONTENTS CONTRIBUTORS LIST vii PREFACE xi 1 Introduction to Electrochemically Active Biofilms 1 Jerome T. Babauta and Haluk Beyenal 2 Theoretical and Practical Considerations for Culturing Geobacter Biofilms in Microbial Fuel Cells and Other Bioelectrochemical Systems 37 Allison M. Speers and Gemma Reguera 3 Microbial Community Characterization on Polarized Electrode Surfaces 61 John M. Regan and Hengjing Yan 4 Characterization of Electrode-Associated Biomass and Microbial Communities 83 Orianna Bretschger, Crystal Snowden, Lisa McDonald, Shino Suzuki, and Shun’ichi Ishii 5 Biofilm Electrochemistry 121 Jerome T. Babauta and Haluk Beyenal vi CONTENTS 6 Theory of Redox Conduction and The Measurement of Electron Transport Rates Through Electrochemically Active Biofilms 177 Darryl A. Boyd, Rachel M. Snider, Jeffrey S. Erickson, Jared N. Roy, Sarah M. Strycharz-Glaven, and Leonard M. Tender 7 Electronic Conductivity in Living Biofilms: Physical Meaning, Mechanisms, and Measurement Methods 211 Nikhil S. Malvankar and Derek R. Lovley 8 Electrochemical Impedance Spectroscopy as A Powerful Analytical Tool for The Study of Microbial Electrochemical Cells 249 Rachel A. Yoho, Sudeep C. Popat, Francisco Fabregat-Santiago, Sixto Giménez, Annemiek Ter Heijne, and César I. Torres 9 Mathematical Modeling of Extracellular Electron Transfer in Biofilms 281 Ryan Renslow, Jerome Babauta, Cornelius Ivory, Haluk Beyenal, Jim Schenk, Andrew Kuprat and Jim Fredrickson 10 Applications of Bioelectrochemical Energy Harvesting in The Marine Environment 345 Clare E. Reimers 11 Large-Scale Benthic Microbial Fuel Cell Construction, Deployment, and Operation 367 Jeff Kagan, Lewis Hsu, and Bart Chadwick INDEX 393 CONTRIBUTORS LIST Jerome T. Babauta, The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA, USA Haluk Beyenal, The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA, USA Darryl A. Boyd, National Research Council, Washington, DC, USA Orianna Bretschger, Microbial and Environmental Genomics Group, J. Craig Ven- ter Institute, San Diego, CA, USA Bart Chadwick, Space and Naval Warfare Systems Center Pacific, San Diego, CA, USA Jeffrey S. Erickson, Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, DC, USA Francisco Fabregat-Santiago, Grup de Dispositius Fotovoltaics i Optoelectrònics, Universitat Jaume I, Spain Jim Fredrickson, Biological Sciences Division, Pacific Northwest National Labora- tory, Richland, WA, USA Sixto Giménez, Grup de Dispositius Fotovoltaics i Optoelectrònics, Universitat Jaume I, Spain Annemiek ter Heijne, Sub-department of Environmental Technology, Wageningen University, Netherlands viii CONTRIBUTORS LIST Lewis Hsu, Space and Naval Warfare Systems Center Pacific, San Diego, CA, USA Shun’ichi Ishii, Microbial and Environmental Genomics Group, J. Craig Venter Institute, San Diego, CA, USA Cornelius Ivory, The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA, USA Jeff Kagan, Space and Naval Warfare Systems Center Pacific, San Diego, CA, USA Andrew Kuprat, Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA Derek R. Lovley, Department of Microbiology, University of Massachusetts, Amherst, USA Nikhil S. Malvankar, Department of Microbiology, University of Massachusetts, Amherst, USA Lisa McDonald, Microbial and Environmental Genomics Group, J. Craig Venter Institute, San Diego, CA, USA Sudeep C. Popat, Swette Center for Environmental Biotechnology, Biodesign Insti- tute, Arizona State University, USA John Regan, Department of Civil and EnvironmentalEngineering, The Pennsylvania State University, University Park, PA, USA Gemma Reguera, Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA Clare E. Reimers, College of Earth, Ocean and Atmospheric Sciences, Oregon State University, OR, USA Ryan Renslow, Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA Jared N. Roy, George Mason University, Manassas, VA, USA Jim Schenk, The Department of Chemistry, Washington State University, Pullman, WA, USA Rachel M. Snider, Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, SW, Washington, DC, USA; BioTechnology Insititute, University of Minnesota, Saint Paul, MN, USA Crystal Snowden, Microbial and Environmental Genomics Group, J. Craig Venter Institute, San Diego, CA, USA Allison M. Speers, Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA CONTRIBUTORS LIST ix Sarah M. Strycharz-Glaven, Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, DC, USA; BioTechnology Insititute, University of Minnesota, Saint Paul, MN, USA Shino Suzuki, Microbial and Environmental Genomics Group, J. Craig Venter Insti- tute, San Diego, CA, USA Leonard M. Tender, Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, DC, USA; BioTechnology Insititute, University of Minnesota, Saint Paul, MN, USA César
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