Joseph Henry Press 500 Fifth Street, NW Washington, DC 20001 The Joseph Henry Press, an imprint of the National Academies Press, was created with the goal of making books on science, technology, and health more widely available to professionals and the public. Joseph Henry was one of the founders of the National Academy of Sciences and a leader in early American science. Any opinions, findings, conclusions, or recommendations expressed in this volume are those of the author and do not reflect the views of the National Academy of Sciences or its affiliated institutions. Library of Congress Cataloging-in-Publication Data Friend, Tim. The third domain : the untold story of archaea and the future of biotechnology / Tim Friend. p. cm. Includes bibliographical references and index. ISBN 978-0-309-10237-7 (hardcover) 1. Archaeobacteria—History. 2. Archaeobacteria—Biotechnology. I. Title. QR82.A69F75 2007 579.3′21—dc22 2007006291 Cover design by Michele de la Menardiere. Cover image © Eye of Science/Science Photo Library. Copyright 2007 by Tim Friend. All rights reserved. Printed in the United States of America To Robin, for a new path. 1 Life in the Outer Limits 1 2 Bug Hunt 32 3 What the Heck Is It? 59 4 The Witch’s Garden 97 5 Rust Never Sleeps 129 6 Us . . . and Them 162 7 Carpe Diem 191 8 Money for Nothin’, Bugs for Free 228 Notes 255 Acknowledgments 273 Index 277 vii And now for something completely different. Monty Python The microbial stench of the Harlem Meer is soaked into our wetsuits, even our skin. Long green strands of algae cling to our heads, shoul- ders, and arms as we rise from the water, giving the appearance and presumably the odor of sea monsters. Ever see Creature from the Black Lagoon? “Not since the beginning of time has the world beheld terror like this!” Yeah, well. Go scuba diving in Central Park. I have just finished collecting from the Harlem Meer the last samples of microorganisms for this mostly science and partly adven- ture tale about the discovery of a strange form of microbial life called the archaea. The Harlem Meer is a small lake in the northeast corner of Central Park. It is by far the nastiest water in which I’ve had the plea- sure to dive. Water leaking around the mouthpiece of my regulator has left a lingering, tangy taste, and perhaps a burning sensation in the back of my throat. The palate suggests hydrocarbons, metals, and something awfully organic. No doubt the samples of filthy sludge and turbid water collected into ziplock baggies and plastic bottles will con- tain many interesting microbes. The archaea—pronounced “ar-kee-ah”—have been found thriv- 1