LIFE’S ENGINES Science Essentials Books in the Science Essentials series bring cutting-e dge science to a general audience. The series provides the foundation for a better understanding of the scientific and technical advances changing our world. In each volume, a prominent scientist— chosen by an advisory board of National Academy of Sciences members—conveys in clear prose the fundamental knowledge underlying a rapidly evolving field of scientific endeavor. The Great Brain Debate: Nature or Nurture, by John Dowling Memory: The Key to Consciousness, by Richard F. Thompson and Stephen Madigan The Faces of Terrorism: Social and Psychological Dimensions, by Neil J. Smelser The Mystery of the Missing Antimatter, by Helen R. Quinn and Yossi Nir The Long Thaw: How Humans Are Changing the Next 100,000 Years of Earth’s Climate, by David Archer The Medea Hypothesis: Is Life on Earth Ultimately Self- Destructive? by Peter Ward How to Find a Habitable Planet, by James Kasting The Little Book of String Theory, by Steven S. Gubser Enhancing Evolution: The Ethical Case for Making Better People, by John Harris Nature’s Compass: The Mystery of Animal Navigation, by James L. Gould and Carol Grant Gould Heart of Darkness: Unraveling the Mysteries of the Invisible Universe, by Jeremiah P. Ostriker and Simon Mitton Oxygen: A Four Billion Year History, by Donald C. Canfield The Cosmic Cocktail: Three Parts Dark Matter, by Katherine Freese Life’s Engines: How Microbes Made Earth Habitable, by Paul G. Falkowski L I F E ’ S E N G I N E S How Microbes Made Earth Habitable Paul G.  Falkowski Princeton University Press Princeton and Oxford Copyright © 2015 by Princeton University Press Published by Princeton University Press, 41 William Street, Princeton, New Jersey 08540 In the United Kingdom: Princeton University Press, 6 Oxford Street, Woodstock, Oxfordshire OX20 1TW press.princeton.edu Jacket Art: Green plant © Pasko Maksim/Shutterstock, E. coli bacteria © Mirumur/ Shutterstock, world © Ase/Shutterstock. All Rights Reserved Library of Congress Cataloging- in- Publication Data Falkowski, Paul G., author. Life’s engines: how microbes made Earth habitable / Paul G. Falkowski. pages cm. - - (Science essentials) Includes bibliographical references and index. ISBN 978-0-691-15537-1 (hardcover: acid- free paper) - - ISBN 0-691-15537-2 (hardcover: acid- free paper) 1. Microorganisms- - Evolution. 2. Bacteria- - Evolution. 3. Microbial genetics. 4. Life (Biology) I. Title. QR13.F35 2015 579- - dc23 2014036615 British Library Cataloging- in- Publication Data is available This book has been composed in Goudy Old Style Printed on acid- free paper. ∞ Printed in the United States of America 1 3 5 7 9 10 8 6 4 2 To my parents, Ed and Helen, my wife and friend, Sari Ruskin, and our daughters, Sasha and Mirit Contents Acknowledgments ix Prologue 1 CHAPTER 1 The Missing Microbes 9 CHAPTER 2 Meet the Microbes 23 CHAPTER 3 The World before Time 40 CHAPTER 4 Life’s Little Engines 47 CHAPTER 5 Supercharging the Engines 68 CHAPTER 6 Protecting the Core Genes 91 CHAPTER 7 Cell Mates 108 CHAPTER 8 Supersizing in Wonderland 124 CHAPTER 9 The Fragile Species 145 CHAPTER 10 The Tinkerers 161 CHAPTER 11 Microbes on Mars and Butterflies on Venus? 173 Further Readings 187 Index 191 Acknowledgments I had been thinking about this book for some time and wrote it in fits and starts over a period of almost two years. The core ideas were developed as an outgrowth of a course I teach every year at Rutgers, History of the Earth Systems, but I didn’t want to write another textbook. I wanted to reach a wider readership and to help elucidate what we know, and per- haps more important, what we don’t know, about the role of microbes in making Earth a habitable planet. The lion’s share of the work was done while I was on sabbatical at the Radcliffe Institute for Advanced Studies at Harvard University. I am extremely grateful to my hosts at the insti- tute and my fellow Fellows for reading and commenting on the first few chapters. I especially thank Ray Jayawardhana (Ray Jay), Tamar Schapiro, Benny Shilo, and Alessandra Buonanno for helping me in the early days. I am indebted to my friend and colleague, Andy Knoll, at Harvard, for encouraging and critiquing my early chapters and for many discussions while I was in Cambridge, Massachusetts. I thank my late friend, Toshiro Saino, who invited me to give a series of lectures at Nagoya University in 2006. Early on, the lectures in Japan helped me focus on structuring this book. Conversations with many people over the years helped me shape my ideas about the role of microbes in the origins of life on this planet. I thank Tom Fenchel and Ed Delong for collaborating with me on a paper describing the role of microbes in maintaining biogeochemical cycles; the basis of that paper was critical in helping me develop several chapters in this book. The late Lynn Margulis was extremely supportive, and we had many discussions over dinner about symbioses. Joe Kirschvink and Minik Rosing helped me understand what tales very old rocks can tell. Many people were extremely helpful in reading chapters and giving constructive comments; I am especially grateful to Sam Elworthy while