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.
Table of Contents
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: rRNAÂ]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 SingleÂ]Cell Microbial Oceanography 24
1.4.2 Toward Understanding CellÂ]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 HIGHÂ]THROUGHPUT SEQUENCING 47
Carlos PedrósÂ]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 SingleÂ]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, MicrobeÂ]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 CultivationÂ]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 SingleÂ]Carbon Compounds 139
4.6.4 Uncovering Suspected and Surprising Temporal Rhythms 139
4.7 Summary 141
4.8 Acknowledgments 141
4.9 References 142
5 ADVANCES IN MICROBIAL ECOLOGY FROM MODEL MARINE BACTERIA: BEYOND THE ESCHERICHIA COLI PARADIGM 149
Sandra MartínezÂ]García and Jarone Pinhassi
5.1 Introduction 149
5.2 Cultivation Approaches 153
5.3 Lessons Learned from Ecophysiological Response Experiments with Cultivated Bacteria 155
5.3.1 Nutrient Cycling (C, N, P, S, and Micronutrients) 155
5.3.2 Photoheterotrophy in Marine Bacteria 163
5.3.3 Microbial Interactions 166
5.3.4 PhageÂ]Host Model Systems in Cyanobacteria and Heterotrophic Bacteria 168
5.3.5 DeepÂ]Sea Bacteria 171
5.4 Concluding Remarks 172
5.5 Summary 174
5.6 Acknowledgments 175
5.7 References 175
6 AN INSEPARABLE LIAISON: MARINE MICROBES AND NONLIVING ORGANIC MATTER 189
Thorsten Dittmar and Carol Arnosti
6.1 An Inseparable Liaison: Marine Microbes and Nonliving Organic Matter 189
6.2 Marine Carbon Reservoirs 192
6.3 Biogeochemical Cycles and Their Microbial Engines 195
6.3.1 Surface Ocean Cycling 195
6.3.2 Particle Formation and Flux 197
6.3.3 Cycling in Sediments 198
6.4 Driving Forces for Turnover Kinetics 200
6.5 Spatial and Temporal Changes in Organic Matter and Microbial Communities 209
6.5.1 Terrestrial Inputs and Transformations 209
6.5.2 Variability in Primary Productivity and Microbial Communities 210
6.5.3 BroadÂ]Scale Patterns of Microbial Community Composition and Activities 211
6.6 The Challenge for Future Research: Understanding the Functional Network of Marine Microbes and Organic Molecules 214
6.7 Summary 217
6.8 Acknowledgments 218
6.9 References 218
7 MICROBIAL ECOLOGY AND BIOGEOCHEMISTRY OF OXYGENÂ]DEFICIENT WATER COLUMNS 231
Klaus Jürgens and Gordon T. Taylor
7.1 Introduction 231
7.2 Current Trends 233
7.3 Characterizing Oxygen Deficiency: Terms and Definitions 234
7.4 Types of OxygenÂ]Deficient Aquatic Systems 237
7.5 PhysicoÂ]Chemical Profiles as Indicators of Biogeochemical Zones 240
7.6 General Considerations of Microbial Metabolism in ODWCs 243
7.7 Biogeochemical Cycles in OxygenÂ]Deficient Systems and Major Prokaryotes Involved 249
7.7.1 Carbon Cycle 252
7.7.2 Nitrogen Cycle 254
7.7.3 Sulfur Cycle 261
7.7.4 Trace Metal Cycling (with a Focus on Manganese) 264
7.8 Microbial Food Webs in ODWCs 265
7.9 Summary 272
7.10 Acknowledgments 273
7.11 References 273
8 THE OCEAN’S MICROSCALE: A MICROBE’S VIEW OF THE SEA 289
Justin R. Seymour and Roman Stocker
8.1 Introduction 289
8.2 The Microscale Physics of the Pelagic Ocean 292
8.2.1 The Importance of CellÂ]toÂ]Cell Distance 292
8.2.2 A World Dominated by Diffusion 295
8.2.3 The Effects of Turbulence at the Microscale 299
8.2.4 Other Effects of Flow on Marine Microbes 301
8.3 Particles, Patches, and Phycospheres 302
8.3.1 Particles as Resource Islands 302
8.3.2 A Continuum of Organic Matter? 303
8.3.3 Microbial Processes Create Patchiness 305
8.3.4 The Phycosphere 306
8.4 Motility and Chemotaxis 306
8.4.1 Motility in the Ocean 307
8.4.2 Chemotaxis to Microscale Hotspots 313
8.5 Microscale Microbial Interactions 319
8.5.1 Quorum Sensing in Microscale Hotspots 319
8.5.2 Antagonistic Interactions within Microscale Habitats 321
8.5.3 Symbiosis within the Phycosphere 322
8.6 Microbial Metabolic Adaptions to Microscale Heterogeneity in Seawater 325
8.7 Biogeochemical Implications of Microscale Interactions 327
8.7.1 Phytoplankton Production 327
8.7.2 Carbon Cycling 328
8.7.3 Nitrogen Cycling 329
8.7.4 Sulfur Cycling 330
8.8 Summary 331
8.9 Acknowledgments 332
8.10 References 332
9 ECOLOGICAL GENOMICS OF MARINE VIRUSES 345
Jennifer R. Brum and Matthew B. Sullivan
9.1 Introduction 345
9.2 Genomics of Isolated Marine Viruses 348
9.3 Investigating Viral Community Diversity in Nature 350
9.4 Marine Viral Community Diversity and Structure 351
9.4.1 Estimating the Size of the Global Virome 353
9.4.2 Estimating Viral Richness 354
9.4.3 Marine Viral Community Structure and Ecological Drivers 354
9.5 DepthÂ]Related Patterns Emerging from Analysis of Marine Viral Metagenomic Data Sets 356
9.6 Emerging Temporal Patterns in Marine Viral Communities 359
9.7 Annotating the Unknown: The Need for Creative Solutions 361
9.8 Investigation of VirusÂ]Host Interactions in the Wild 364
9.9 Future Challenges in Marine Viral Ecology 365
9.9.1 The Need to Capture Other Viral Types 365
9.9.2 Moving Beyond UpperÂ]Ocean Waters 366
9.9.3 Making the GenesÂ]toÂ]Ecosystems Leap to Evaluate Processes 367
9.10 Summary 368
9.11 Acknowledgments 369
9.12 References 369
10 MICROBIAL PHYSIOLOGICAL ECOLOGY OF THE MARINE PHOSPHORUS CYCLE 377
Sonya T. Dyhrman
10.1 Introduction 377
10.2 Methodological Advances and Challenges 379
10.3 Phosphorus Biogeochemistry 382
10.3.1 The Phosphorus Cycle 382
10.3.2 Sources and Sinks 382
10.3.3 Phosphorus Stoichiometry 383
10.4 Phosphorus in the Cell 383
10.4.1 Phosphorus Biochemicals 383
10.4.2 Phosphorus Redox State 385
10.4.3 Phosphorus Bond Classes 386
10.5 Microbial Biogeochemistry of Phosphorus Bond Types 386
10.5.1 Polyphosphate 387
10.5.2 Phosphoester 389
10.5.3 Phosphonate 390
10.6 Inorganic Phosphorus Utilization 391
10.6.1 Phosphate Uptake 391
10.6.2 Polyphosphate Utilization 393
10.6.3 Phosphite Metabolism 394
10.7 Organic Phosphorus Utilization 395
10.7.1 Phosphoester Enzymes 395
10.7.2 Phosphonate Enzymes 400
10.8 Phosphorus Stress Responses 402
10.8.1 Phosphorus Stress Signaling 405
10.8.2 Phosphorus Sparing or Recycling 406
10.8.3 HighÂ]Affinity or Increased Phosphate Transport 410
10.8.4 Utilization of Alternative Phosphorus Forms 410
10.9 Case Studies in Phosphorus Physiology 411
10.9.1 Bacteria: Pelagibacter 411
10.9.2 Diazotroph: Trichodesmium 413
10.9.3 Archaea: Nitrosopumilus 414
10.9.4 Microeukaryote: Thalassiosira 415
10.10 Case Studies with Different Systems 416
10.10.1 Western North Atlantic 416
10.10.2 Mediterranean 417
10.10.3 Gulf of Mexico 418
10.11 Summary 419
10.12 Acknowledgments 420
10.13 References 420
11 PHYTOPLANKTON FUNCTIONAL TYPES: A TRAIT PERSPECTIVE 435
Andrew J. Irwin and Zoe V. Finkel
11.1 What Are Functional Types? 435
11.2 The Major Functional Traits 437
11.2.1 What Is a Trait? 437
11.2.2 Types of Traits 438
11.2.3 Size as a Master Trait 443
11.2.4 Trait TradeÂ]Offs 445
11.2.5 Trait Differences across Phytoplankton Functional Types 445
11.3 Challenges Using Traits to Represent Functional Types 446
11.3.1 Challenges Estimating Average Trait Values for Phytoplankton Functional Types 446
11.3.2 Challenges Posed by Acclimation and Adaptation 449
11.4 Using Field Data to Identify Relevant Traits and Estimate Trait Values 450
11.4.1 Why Use Field Data? 450
11.4.2 How Can We Identify Traits and Niches of Phytoplankton Functional Types from Field Data? 452
11.4.3 Are Phytoplankton Niches Stable over Time? 453
11.5 Should We Model Functional Types or Individual Species? 455
11.6 A Way Forward 457
11.7 Summary 459
11.8 References 459
12 THEORETICAL INTERPRETATIONS OF SUBTROPICAL PLANKTON BIOGEOGRAPHY 467
Michael J. Follows, Stephanie Dutkiewicz, Ben A. Ward and Christopher N. Follett
12.1 Introduction: Phytoplankton Biogeography in the Subtropical Ocean 468
12.2 Resource Competition, Fitness, and Cell Size 476
12.3 Coexisting Size Classes: Predation Levels the Playing Field 481
12.4 Niche Differentiation and Resource Ratio Theory 483
12.4.1 Resource Ratio Theory for Nitrogen Fixation 485
12.4.2 Predicted Global Biogeography of Nitrogen Fixation 488
12.5 Discussion and Outlook 488
12.5.1 Outlook 489
12.6 Summary 490
12.7 Acknowledgments 490
12.8 References 491
INDEX 495
