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Microbes from Hell

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Microbes from Hell Microbes from Hell Microbes from Hell Patrick Forterre Translated by Teresa Lavender Fagan The University of Chicago Press Chicago and London The University of Chicago Press, Chicago 60637 The University of Chicago Press, Ltd., London © 2016 by The University of Chicago All rights reserved. Published 2016. Printed in the United States of America Originally published as Microbes de l’enfer by Patrick Forterre. © Editions Belin, 2007. 25 24 23 22 21 20 19 18 17 16 1 2 3 4 5 ISBN- 13: 978- 0- 226- 26582- 7 (cloth) ISBN- 13: 978- 0- 226- 26596- 4 (e- book) DOI: 10.7208/chicago/9780226265964.001.0001 Library of Congress Cataloging- in- Publication Data Names: Forterre, Patrick, author. | Fagan, Teresa Lavender, translator. Title: Microbes from hell / Patrick Forterre ; translated by Teresa Lavender Fagan. Other titles: Microbes de l’enfer. English Description: Chicago ; London : University of Chicago Press, 2016. | © 2016 | Includes bibliographical references and index. Identifiers: LCCN 2016009697 | ISBN 9780226265827 (cloth : alkaline paper) | ISBN 9780226265964 (e- book) Subjects: LCSH: Thermophilic microorganisms. | Microorganisms— Effect of heat on. Classification: LCC QR84.8.F6713 2016 | DDC 579.3/17— dc23 LC record available at http:// lccn .loc .gov /2016009697 ♾ This paper meets the requirements of ANSI/NISO Z39.48- 1992 (Permanence of Paper). Children of steam and scalded rock, a story you have to tell, Writ in the glare of sunshine bright, Sculptured and etched in marble white, Illuminated in colors bold, Richer than ever parchment old, Children of steam and scalded rock, what is the story you have to tell? Our legends are old, of greater age than the mountains round about. We have kept our secrets epochs long, They are not to be read by the passing throng. It is nothing to us what men may say. If they wish our story the price they must pay In hard brain work, ere the tales are told. We challenge mankind to draw them out. Children of steam and scalded rock, your challenge must rest for the present age. I have scarcely broken the outer crust That covers the greater truth, but I trust Some man will follow and therein find Knowledge, that to the Present shall bind The Past with cords wherein entwine Threads of the perfect truth, divine. Children of steam and scalded rock, some man to come will accept thy gage. A poem by Bradley Moore Davis, University of Chicago, published in his 1897 paper in the journal Science and describing for the first time microbes present in Yellowstone hot springs. This book will tell you the story of those who “accept thy gage.” Contents Prologue 1 1 A Bit of History: Microbes and Humans 6 2 Hunting Hyperthermophiles and Their Viruses: From the Great Depths to the Laboratory 51 3 How Do You Live in Hell? 90 4 The Universal Tree of Life: Where to Place Microbes from Hell and Their Viruses? 131 5 The Universal Tree of Life: Are Microbes from Hell Our Ancestors? 181 Epilogue 228 Acknowledgments 231 Notes 233 References 247 Index 267 Prologue The souls of the damned writhe in pain in the cauldrons of hell. Life appears to be incompatible with the flames of Satan. Plunge a crab into a pot of boil- ing water and it comes out cooked— but dead. Plunge your own finger in and the pain is unbearable. It’s indisputable: even if we like heat, preferably in the shade on a beach, we must stay within the limits of what is reasonable. And yet, in the last thirty years, scientists have discovered microbes that thrive in temperatures that exceed those of the hottest deserts in the world. These creatures, whose existence is revealed only under a microscope, live in places that humans have equated with the gateway to hell. They are found in Solfa- tara, near Naples, Italy, which the ancient Greeks believed was the home of Charon, whose boat transported the souls of the dead on their final voyage, and in Iceland, the island where Jules Verne’s heroes journeyed to the center of the earth. These microscopic single- celled organisms have telling names, such as Acidianus infernus, which likes both “infernal” temperatures and ex- treme acidity, or Pyrococcus abyssi, the “burning shell of the abyss.” These are thermophile microbes (from the Greek therme, “heat,” and phylos, “that which loves”). The most infernal among them have been baptized as “hyper- thermophile” microbes because these amazing beings, which love the highest temperatures, flourish only between 80 and 110°C and freeze below 70°C. These microbes from hell, whose existence was unknown to scientists until relatively recently, are today at the heart of particularly active research. International meetings have been devoted to them every two years since 1990, bringing together first dozens, then hundreds, of scientists from throughout the world. Why such passion for living beings so different from us? Some evolutionists believe that thermophile and hyperthermophile microbes can teach us a lot about the way life appeared on our planet, at a time when it 2 prologue perhaps resembled hell more than it did heaven. Others (sometimes the same ones) think the microbes that live in such extreme environments will help us determine the conditions necessary and sufficient for a planet to sustain life. Ultimately, all the specialists who study these microbes from hell wonder how they manage to thrive in places where all other forms of life are destroyed in a matter of seconds. The scientists’ goal is to discover all the tricks these organisms have invented during evolution to protect their molecules from the destructive effects of extremely high temperatures. They tell themselves that these inhabitants of hot environments must be hiding many secrets that are only waiting to be brought to light by imaginative and persistent scientists, who can then make wonderful discoveries based on them. The biotechnology industry and those who want to put microbes to work to replace traditional chemical products with more “green” chemicals are also very interested in these microbes from hell. They hope to be able to use the extraordinary resistance of the microbes’ proteins for treatments that destroy “classic” proteins. These hopes are not utopian. One of the greatest techno- logical revolutions known to biology in the past twenty- five years was ac- complished thanks to an isolated protein of a thermophile microbe. This was the perfection in 1987 of a technique called PCR— polymerase chain reaction. This technique enables the controlled and specific amplification of any area of the DNA molecule: the famous double helix that contains our genetic data. This amplification alone enables us to obtain enough material to make the DNA molecule “speak.” PCR has countless applications in biology, but also in medicine (in particular, for the diagnosis of hereditary diseases or viral infec- tions) and even in criminology. What is the connection between PCR and microbes from hell? The tech- nique requires the use of an enzyme, DNA polymerase, capable of reproduc- ing an identical DNA molecule by copying the two strands of the double helix (a chemical reaction corresponding to a polymerization). The amplification of DNA is achieved through the many cycles of chain reactions, during which the quantity of DNA is doubled each time. Each of these cycles includes an incubation stage at 90°C to separate the two strands of the double helix. The DNA polymerase used must thus be particularly strong at high temperatures. Here is the problem: at 90°C, the proteins are irrevocably destroyed— except, of course, those of microbes from hell. The DNA polymerase used most often today to achieve the amplifica- tion of DNA through PCR is extracted from a thermophile bacterium called Thermus aquaticus (“hot microbe that lives in water”), discovered in 1967 by American microbiologist Thomas Brock in the hot springs of Yellowstone National Park. Without the curiosity and stubbornness of this scientist, many prologue 3 scientific discoveries would not have seen the light of day, many murderers would have escaped justice, and many innocents sentenced to death would have been executed. The patents filed for the method that enables the amplification of DNA by PCR using the isolated enzyme of Thermus aquaticus and for the method that enables the amplification of DNA have for years brought in hundreds of millions of dollars every year. We now understand better why thermophiles and hyperthermophiles have been riding so high. For some, these microbes are veritable gold mines. In this work I will not, however, focus on this aspect of things, because a choice must be made, and I am not a specialist in bio- technology. Beyond being a gold mine for some and a source of innovation beneficial to all, microbes from hell are above all a passion for most of the sci- entists who are interested in them. I have therefore chosen to show why these living beings excite the curiosity of scientists and how this curiosity bears fruit. When Brock, while on vacation in Yellowstone, asked himself if the hot springs in the park might contain living beings, he couldn’t have imagined that Thermus aquaticus would one day be a goose laying golden eggs. He was simply inspired by the desire to understand the world that surrounded and fascinated him. It was again curiosity that led two German biologists who will accompany us throughout this book, Wolfram Zillig and Karl Stetter, to travel the globe looking for creatures able to live at increasingly high temperatures. It is they who discovered hyperthermophiles. We will see how their research revealed a new world that until then had gone undetected, thus pushing the limits of the living being beyond anything we could have ever dreamed of before.
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