Contents

Contributors   ··

Preface    ··

Introduction   Darwin and Microbiology    1

                        Roberto Kolter and Stanley Maloy

Chapter 1       Evolution in Action: A 50,000-Generation Salute to Charles Darwin    9

                        Richard E. Lenski

Chapter 2       Minimal Genomes and Reducible Complexity    17

                        Andrés Moya

Chapter 3       Lady Lumps’s Mouthguard    25

                        Jessica Green

Chapter 4       Trying To Make Sense of the Microbial Census    31

                        Mitchell L. Sogin

Chapter 5       The View from Below    37

                        Margaret Riley and Robert Dorit

Chapter 6       Running Wild with Antibiotics    43

                        Roberto Kolter

Chapter 7       Antibiotic Resistance    49

                        Diarmaid Hughes

Chapter 8       Bacteria Battling for Survival    59

                        Thomas M. Schmidt

Chapter 9       Phage: An Important Evolutionary Force Darwin Never Knew    65

                        Forest Rohwer

Chapter 10     The Struggle for Existence: Mutualism    71

                        Paul E. Turner

Chapter 11     The Secret Social Lives of Microorganisms    77

                        Kevin R. Foster

Chapter 12     Microbes and Microevolution    85

                        Evgeni Sokurenko

Chapter 13     Unnecessary Baggage    93

                        Stanley Maloy and Guido Mora

Chapter 14     Bacterial Adaptation: Built-In Responses and Random Variations    99

                        Josep Casadesús

Chapter 15     The Impact of Differential Regulation on Bacterial Speciation    109

                        Eduardo A. Groisman

Chapter 16     An Accidental Evolutionary Biologist: GASP, Long-Term Survival, and Evolution    115

                        Steven E. Finkel

Chapter 17     How Bacteria Revealed Darwin’s Mistake (and Got Me To Read On the Origin of Species)    123

                        John R. Roth

Chapter 18     The Role of Conjugation in the Evolution of Bacteria    133

                        Fernando de la Cruz

Chapter 19     Do Bacteria Have Sex?    139

                        Rosemary J. Redfield

Chapter 20     Better than Sex    145

                        Harald Brüssow

Chapter 21     Darwin in My Lab: Mutation, Recombination, and Speciation    151

                        Miroslav Radman

Chapter 22     Sexual Difficulties    159

                        Howard Ochman

Chapter 23     Unveiling Prochlorococcus: The Life and Times of the Ocean’s Smallest Photosynthetic Cell    165

                        Sallie W. Chisholm

Chapter 24     Deciphering the Language of Diplomacy: Give and Take in the Study of the Squid-Vibrio Symbiosis    173

                        Margaret McFall-Ngai and Ned Ruby

Chapter 25     The Tangled Banks of Ants and Microbes    181

                        Cameron R. Currie

Chapter 26     Microbial Symbiosis and Evolution    191

                        Nancy A. Moran

Chapter 27     Coevolution of Helicobacter pylori and Humans    197

                        Martin J. Blaser

Chapter 28     The Library of Maynard-Smith: My Search for Meaning in the Protein Universe    203

                        Frances H. Arnold

Chapter 29     In Pursuit of Billion-Year-Old Rosetta Stones    209

                        Dianne K. Newman

Chapter 30     The Deep History of Life    217

                        Andrew H. Knoll

Chapter 31     A Glimpse into Microevolution in Nature: Adaptation and Speciation of Bacillus simplex from “Evolution Canyon”    225

                        Johannes Sikorski

Chapter 32     On the Origin of Bacterial Pathogenic Species by Means of Natural Selection: A Tale of Coevolution    233

                        Philippe J. Sansonetti

Chapter 33     The Evolution of Diversity and the Emergence of Rules Governing Phenotypic Evolution    241

                        Paul B. Rainey

Chapter 34     The Christmas Fungus on Christmas Island    251

                        Anne Pringle

Chapter 35     A New Age of Naturalists    255

                        Rachel A. Whitaker

Chapter 36     The Ship That Led to Shape    263

                        Kevin D. Young

Chapter 37     Postphylogenetics    269

                        W. Ford Doolittle

Chapter 38     Irreducible Complexity? Not!    275

                        David F. Blair and Kelly T. Hughes

Chapter 39     Many Challenges to Classifying Microbial Species    281

                        Stephen Giovannoni