Note: Intro -- TITLE PAGE -- TABLE OF CONTENTS -- PREFACE -- CONTRIBUTORS -- 1 INTRODUCTION -- 1.1 INTRODUCTION -- 1.2 A BRIEF HISTORY OF MARINE MICROBIAL ECOLOGY -- 1.3 AN ASSESSMENT OF CURRENT MARINE MICROBIAL ECOLOGY -- 1.4 THE FUTURE OF MARINE MICROBIAL ECOLOGY -- 1.5 SUMMARY -- 1.6 REFERENCES -- 2 MARINE MICROBIAL DIVERSITY AS SEEN BY HIGH‐THROUGHPUT SEQUENCING -- 2.1 DIVERSITY -- 2.2 THE METHODS -- 2.3 THE USE OF SEQUENCES AS PROXIES FOR TAXA -- 2.4 DIVERSITY AFTER HTS -- 2.5 CONCLUSION -- 2.6 SUMMARY -- 2.7 ACKNOWLEDGMENTS -- 2.8 REFERENCES -- 3 ECOLOGICAL SIGNIFICANCE OF MICROBIAL TROPHIC MIXING IN THE OLIGOTROPHIC OCEAN -- 3.1 OLIGOTROPHIC OCEANIC GYRES: THE MOST EXTENSIVE, MICROBE‐DOMINATED BIOME ON EARTH -- 3.2 MICROBIAL COMPOSITION OF THE SUBTROPICAL GYRES -- 3.3 PROKARYOTIC PHOTOHETEROTROPHY IN GYRES: THE ABILITY TO USE LIGHT ENERGY AND TO TAKE UP ORGANIC MOLECULES SIMULTANEOUSLY -- 3.4 EUKARYOTIC MIXOTROPHY IN GYRES: THE ABILITY TO USE LIGHT ENERGY AND SIMULTANEOUSLY PREY ON BACTERIOPLANKTON -- 3.5 HOW DO PHOTOHETEROTROPHY AND MIXOTROPHY AFFECT THE COEXISTENCE OF BACTERIA AND EUKARYOTES IN GYRES? -- 3.6 KNOWLEDGE GAPS -- 3.7 SUMMARY -- 3.8 ACKNOWLEDGMENTS -- 3.9 REFERENCES -- 4 METATRANSCRIPTOMICS AND METAPROTEOMICS -- 4.1 INTRODUCTION TO MARINE "OMICS" AND BIG DATA -- 4.2 OVERVIEW OF THE METATRANSCRIPTOMICS APPROACH -- 4.3 OVERVIEW OF THE METAPROTEOMICS APPROACH -- 4.4 KEY CONSIDERATIONS IN DETECTING COMMUNITY ECOSYSTEM FUNCTIONS -- 4.5 IMPORTANCE OF CULTIVATION‐BASED STUDIES, REPLICATION, AND QUANTIFICATION -- 4.6 MARINE MICROBIAL COMMUNITY TRANSCRIPTOMICS AND PROTEOMICS -- 4.7 SUMMARY -- 4.8 ACKNOWLEDGMENTS -- 4.9 REFERENCES -- 5 ADVANCES IN MICROBIAL ECOLOGY FROM MODEL MARINE BACTERIA -- 5.1 INTRODUCTION -- 5.2 CULTIVATION APPROACHES -- 5.3 LESSONS LEARNED FROM ECOPHYSIOLOGICAL RESPONSE EXPERIMENTS WITH CULTIVATED BACTERIA. , 5.4 CONCLUDING REMARKS -- 5.5 SUMMARY -- 5.6 ACKNOWLEDGMENTS -- 5.7 REFERENCES -- 6 AN INSEPARABLE LIAISON -- 6.1 AN INSEPARABLE LIAISON: MARINE MICROBES AND NONLIVING ORGANIC MATTER -- 6.2 MARINE CARBON RESERVOIRS -- 6.3 BIOGEOCHEMICAL CYCLES AND THEIR MICROBIAL ENGINES -- 6.4 DRIVING FORCES FOR TURNOVER KINETICS -- 6.5 SPATIAL AND TEMPORAL CHANGES IN ORGANIC MATTER AND MICROBIAL COMMUNITIES -- 6.6 THE CHALLENGE FOR FUTURE RESEARCH: UNDERSTANDING THE FUNCTIONAL NETWORK OF MARINE MICROBES AND ORGANIC MOLECULES -- 6.7 SUMMARY -- 6.8 ACKNOWLEDGMENTS -- 6.9 REFERENCES -- 7 MICROBIAL ECOLOGY AND BIOGEOCHEMISTRY OF OXYGEN‐DEFICIENT WATER COLUMNS -- 7.1 INTRODUCTION -- 7.2 CURRENT TRENDS -- 7.3 CHARACTERIZING OXYGEN DEFICIENCY: TERMS AND DEFINITIONS -- 7.4 TYPES OF OXYGEN‐DEFICIENT AQUATIC SYSTEMS -- 7.5 PHYSICO‐CHEMICAL PROFILES AS INDICATORS OF BIOGEOCHEMICAL ZONES -- 7.6 GENERAL CONSIDERATIONS OF MICROBIAL METABOLISM IN ODWCS -- 7.7 BIOGEOCHEMICAL CYCLES IN OXYGEN‐DEFICIENT SYSTEMS AND MAJOR PROKARYOTES INVOLVED -- 7.8 MICROBIAL FOOD WEBS IN ODWCS -- 7.9 SUMMARY -- 7.10 ACKNOWLEDGMENTS -- 7.11 REFERENCES -- 8 THE OCEAN'S MICROSCALE -- 8.1 INTRODUCTION -- 8.2 THE MICROSCALE PHYSICS OF THE PELAGIC OCEAN -- 8.3 PARTICLES, PATCHES, AND PHYCOSPHERES -- 8.4 MOTILITY AND CHEMOTAXIS -- 8.5 MICROSCALE MICROBIAL INTERACTIONS -- 8.6 MICROBIAL METABOLIC ADAPTIONS TO MICROSCALE HETEROGENEITY IN SEAWATER -- 8.7 BIOGEOCHEMICAL IMPLICATIONS OF MICROSCALE INTERACTIONS -- 8.8 SUMMARY -- 8.9 ACKNOWLEDGMENTS -- 8.10 REFERENCES -- 9 ECOLOGICAL GENOMICS OF MARINE VIRUSES -- 9.1 INTRODUCTION -- 9.2 GENOMICS OF ISOLATED MARINE VIRUSES -- 9.3 INVESTIGATING VIRAL COMMUNITY DIVERSITY IN NATURE -- 9.4 MARINE VIRAL COMMUNITY DIVERSITY AND STRUCTURE -- 9.5 DEPTH‐RELATED PATTERNS EMERGING FROM ANALYSIS OF MARINE VIRAL METAGENOMIC DATA SETS. , 9.6 EMERGING TEMPORAL PATTERNS IN MARINE VIRAL COMMUNITIES -- 9.7 ANNOTATING THE UNKNOWN: THE NEED FOR CREATIVE SOLUTIONS -- 9.8 INVESTIGATION OF VIRUS‐HOST INTERACTIONS IN THE WILD -- 9.9 FUTURE CHALLENGES IN MARINE VIRAL ECOLOGY -- 9.10 SUMMARY -- 9.11 ACKNOWLEDGMENTS -- 9.12 REFERENCES -- 10 MICROBIAL PHYSIOLOGICAL ECOLOGY OF THE MARINE PHOSPHORUS CYCLE -- 10.1 INTRODUCTION -- 10.2 METHODOLOGICAL ADVANCES AND CHALLENGES -- 10.3 PHOSPHORUS BIOGEOCHEMISTRY -- 10.4 PHOSPHORUS IN THE CELL -- 10.5 MICROBIAL BIOGEOCHEMISTRY OF PHOSPHORUS BOND TYPES -- 10.6 INORGANIC PHOSPHORUS UTILIZATION -- 10.7 ORGANIC PHOSPHORUS UTILIZATION -- 10.8 PHOSPHORUS STRESS RESPONSES -- 10.9 CASE STUDIES IN PHOSPHORUS PHYSIOLOGY -- 10.10 CASE STUDIES WITH DIFFERENT SYSTEMS -- 10.11 SUMMARY -- 10.12 ACKNOWLEDGMENTS -- 10.13 REFERENCES -- 11 PHYTOPLANKTON FUNCTIONAL TYPES -- 11.1 WHAT ARE FUNCTIONAL TYPES? -- 11.2 THE MAJOR FUNCTIONAL TRAITS -- 11.3 CHALLENGES USING TRAITS TO REPRESENT FUNCTIONAL TYPES -- 11.4 USING FIELD DATA TO IDENTIFY RELEVANT TRAITS AND ESTIMATE TRAIT VALUES -- 11.5 Should We Model Functional Types or Individual Species? -- 11.6 A WAY FORWARD -- 11.7 SUMMARY -- 11.8 REFERENCES -- 12 THEORETICAL INTERPRETATIONS OF SUBTROPICAL PLANKTON BIOGEOGRAPHY -- 12.1 INTRODUCTION: PHYTOPLANKTON BIOGEOGRAPHY IN THE SUBTROPICAL OCEAN -- 12.2 RESOURCE COMPETITION, FITNESS, AND CELL SIZE -- 12.3 COEXISTING SIZE CLASSES: PREDATION LEVELS THE PLAYING FIELD -- 12.4 NICHE DIFFERENTIATION AND RESOURCE RATIO THEORY -- 12.5 DISCUSSION AND OUTLOOK -- 12.6 SUMMARY -- 12.7 ACKNOWLEDGMENTS -- REFERENCES -- INDEX -- END USER LICENSE AGREEMENT.