Microbial Ecology of the Oceans

The newly revised and updated third edition of the bestselling book on microbial ecology in the oceans

The third edition of Microbial Ecology of the Oceans features new topics, as well as different approaches to subjects dealt with in previous editions. The book starts out with a general introduction to the changes in the field, as well as looking at the prospects for the coming years. Chapters cover ecology, diversity, and function of microbes, and of microbial genes in the ocean. The biology and ecology of some model organisms, and how we can model the whole of the marine microbes, are dealt with, and some of the trophic roles that have changed in the last years are discussed. Finally, the role of microbes in the oceanic P cycle are presented.

Microbial Ecology of the Oceans, Third Edition offers chapters on The Evolution of Microbial Ecology of the Ocean; Marine Microbial Diversity as Seen by High Throughput Sequencing; Ecological Significance of Microbial Trophic Mixing in the Oligotrophic Ocean; Metatranscritomics and Metaproteomics; Advances in Microbial Ecology from Model Marine Bacteria; Marine Microbes and Nonliving Organic Matter; Microbial Ecology and Biogeochemistry of Oxygen-Deficient Water Columns; The Ocean's Microscale; Ecological Genomics of Marine Viruses; Microbial Physiological Ecology of The Marine Phosphorus Cycle; Phytoplankton Functional Types; and more.

• A new and updated edition of a key book in aquatic microbial ecology

• Includes widely used methodological approaches

• Fully describes the structure of the microbial ecosystem, discussing in particular the sources of carbon for microbial growth

• Offers theoretical interpretations of subtropical plankton biogeography

Microbial Ecology of the Oceans is an ideal text for advanced undergraduates, beginning graduate students, and colleagues from other fields wishing to learn about microbes and the processes they mediate in marine systems.

Auteur

About the Editors Josep M. Gasol is a Research Professor at the Institut de Ciències del Mar, CSIC, in Barcelona, Spain. David L. Kirchman is a Professor in the School of Marine Science and Policy at the University of Delaware, USA.

Contenu
PREFACE xiii

CONTRIBUTORS xv

**1 INTRODUCTION: THE EVOLUTION OF MICROBIAL ECOLOGY OF THE OCEAN 1
**Josep M. Gasol and David L. Kirchman

1.1 Introduction 1

1.2 A Brief History of Marine Microbial Ecology 3

1.2.1 Biological Oceanography and Black Box Microbial Ecology 6

1.2.2 Opening the Black Box for Variability in Activity and Growth Rates 9

1.2.3 The Molecular Description of Microbial Diversity: rRNA?]Based Approaches 11

1.2.4 The Molecular Description of Microbial Diversity: Whole Organisms and Genomes 14

1.2.5 N2 Fixation Studies as a Model for Marine Microbial Ecology 18

1.3 An Assessment of Current Marine Microbial Ecology 20

1.4 The Future of Marine Microbial Ecology 24

1.4.1 Toward Single?]Cell Microbial Oceanography 24

1.4.2 Toward Understanding Cell?]Cell Interactions 26

1.4.3 Toward Comprehensive Exploration of All Marine Habitats 27

1.4.4 Toward Changing Our View of the Fluxes of C and the Role of the Various Microbes 28

1.4.5 Toward Describing the Unknown Component of Microbial Diversity in the Oceans 29

1.5 Summary 30

1.6 References 31

**2 MARINE MICROBIAL DIVERSITY AS SEEN BY HIGH?]THROUGHPUT SEQUENCING 47
**Carlos Pedrós?]Alió, Silvia G. Acinas, Ramiro Logares and Ramon Massana

2.1 Diversity 47

2.1.1 Mechanisms Promoting Appearance of Novel Taxa 48

2.1.2 Mechanisms Promoting Coexistence 50

2.2 The Methods 53

2.2.1 First Applications of Sequencing Technology to the Marine Environment 55

2.2.2 HTS for Diversity Studies 56

2.2.3 rDNA Tags Extracted from Metagenomes 58

2.2.4 Single?]Cell Genomics 58

2.2.5 Challenges of Processing Sequence Data 59

2.3 The Use of Sequences as Proxies for Taxa 59

2.3.1 Building Taxonomic Units from Sequences 59

2.3.2 Tools for Data Analysis 64

2.3.3 Comparison of Tag Sequences and the Biological Species Concept 65

2.3.4 Contribution of HTS and Genomes to a Novel Definition of Microbial Species 66

2.4 Diversity after HTS 68

2.4.1 One Sample (Alpha Diversity) 68

2.4.2 Comparison of Several Samples (Beta and Gamma Diversity) 71

2.4.3 The Unknown Marine Microbial Diversity 84

2.5 Conclusion 86

2.6 Summary 87

2.7 Acknowledgments 87

2.8 References 87

3 ECOLOGICAL SIGNIFICANCE OF MICROBIAL TROPHIC MIXING IN THE OLIGOTROPHIC OCEAN: THE **ATLANTIC OCEAN CASE STUDIES 99
**Mikhail V. Zubkov and Manuela Hartmann

3.1 Oligotrophic Oceanic Gyres: The Most Extensive, Microbe?]Dominated Biome on Earth 99

3.2 Microbial Composition of the Subtropical Gyres 101

3.3 Prokaryotic Photoheterotrophy in Gyres: The Ability to Use Light Energy and to Take up Organic Molecules Simultaneously 103

3.4 Eukaryotic Mixotrophy in Gyres: The Ability to Use Light Energy and Simultaneously Prey on Bacterioplankton 106

3.5 How Do Photoheterotrophy and Mixotrophy Affect the Coexistence of Bacteria and Eukaryotes in Gyres? 109

3.6 Knowledge Gaps 112

3.7 Summary 114

3.8 Acknowledgments 114

3.9 References 114

4 METATRANSCRIPTOMICS AND METAPROTEOMICS: ELUCIDATING MARINE MICROBIAL ECOSYSTEM **FUNCTIONS 123
**Robert M. Morris

4.1 Introduction to Marine Omics and Big Data 123

4.2 Overview of the Metatranscriptomics Approach 126

4.3 Overview of the Metaproteomics Approach 129

4.4 Key Considerations in Detecting Community Ecosystem Functions 131

4.5 Importance of Cultivation?]Based Studies, Replication, and Quantification 134

4.6 Marine Microbial Community Transcriptomics and Proteomics 134

4.6.1 Primary and Secondary Transporters Signal Shifts in Marine Microbial Communities 136

4.6.2 Significant Photoheterotrophic Contribution to Marine Microbial Communities 137

4.6.3 Microbial Metabolism of Single?]Carbon Compounds 139 4.6.4 U...