Microbial Ecology of the Oceans

by Kirchman, David L.

• ISBN13: 9780470043448
• ISBN10: 047004344X
• Edition: 2nd
• Format: Hardcover
• Copyright: 2008-06-23
• Publisher: Wiley-Liss

Summary

Microbial Ecology of the Oceans, 2nd Edition reviews the basics of marine microbiology, provides a foundation for researchers and students new to the field, and examines the important issues in modern ocean microbial ecology. Explore the latest advances in biological and chemical oceanography and limnology and understand the role of marine microbes and viruses in the oceans. Like the successful first edition, this updated and revised text combines concepts from autoecological studies of individual bacterial groups and from ecological studies of microbial assemblages in the oceans.

Author Biography

David L. Kirchman, PhD, is the former editor-in-chief of the journal Limnology and Oceanography and has published over 100 papers in microbiologyand the marine sciences. He is an internationally recognized authority in microbial ecology and biological oceanography.

Table of Contents

Preface	p. xv
Contributors	p. xvii
Introduction and Overview	p. 1
Eukaryotic Phytoplankton and Cyanobacteria	p. 3
Photoheterotrophic Bacteria	p. 5
Dissolved Organic Material	p. 7
Heterotrophic Bacteria	p. 10
Marine Archaea	p. 13
Heterotrophic Protists	p. 14
Nanoflagellates (2-20 [gamma]m)	p. 14
Microzooplanktonic Protists (20-200 [gamma]m)	p. 16
Dinoflagellates	p. 16
Marine Fungi	p. 16
Marine Viruses	p. 17
N[subscript 2] Fixers	p. 18
Nitrifiers and Other Chemolithotrophs	p. 19
Denitrifiers	p. 20
Concluding Remarks	p. 21
Summary	p. 22
Acknowledgments	p. 22
References	p. 23
Understanding Roles of Microbes in Marine Pelagic Food Webs: A Brief History	p. 27
Introduction	p. 27
Pre-1950s: The Early Years	p. 28
1950-1974	p. 29
1970s-1980s	p. 32
Improvement in Methods	p. 32
Bacterial Abundance	p. 32
Bacterial Activity	p. 33
Marine Heterotrophic Protists	p. 34
The "Microbial Loop"	p. 36
1990-Present: The Molecular Revolution	p. 39
Summary	p. 40
References	p. 41
Bacterial and Archaeal Community Structure and Its Patterns	p. 45
Introduction	p. 45
Major Groups of Prokaryotes in Seawater	p. 47
"Classically" Culturable Bacteria	p. 49
The Roseobacter Clade of Marine Alphaproteobacteria	p. 50
Gammaproteobacteria	p. 51
Bacteroidetes	p. 52
Cyanobacteria	p. 52
"Sea Water" Culturable Bacteria	p. 55
SAR11 Cluster	p. 55
Not-Yet-Cultured Bacteria	p. 57
Marine Gammaproteobacterial Clusters	p. 57
Actinobacteria	p. 58
SAR116 Cluster	p. 59
SAR202	p. 59
Marine Group A	p. 59
Marine Group B	p. 59
Betaproteobacteria	p. 59
Marine Archaea	p. 60
Bacterioplankton Diversity	p. 63
Species Concept	p. 63
Microdiversity	p. 64
Components of Diversity: Richness and Evenness	p. 65
Community Structure: Description and Factors	p. 67
Bottom-Up Control	p. 68
Sideways Control	p. 69
Top-Down Control	p. 70
"Kill the Winner" Hypothesis	p. 71
Temporal Variation (Days to Seasonal)	p. 72
Short-Term Variation	p. 72
Seasonal Variation	p. 72
Spatial Variation	p. 74
Microscale Patterns	p. 74
Global Distribution	p. 75
Latitudinal Gradient and Degree of Endemism	p. 76
Patchiness and Large Eddies	p. 77
Summary	p. 79
References	p. 80
Genomics and Metagenomics of Marine Prokaryotes	p. 91
Introduction	p. 91
The Basics of Prokaryotic Genomics	p. 92
Genome Sequence and Assembly	p. 92
Finding Genes	p. 95
Finding Operons	p. 96
Functional Annotation	p. 96
Tame or Wild? Pure-Culture Genomics Versus Metagenomics	p. 100
Genomics in Marine Microbial Ecology	p. 103
The Ecology of Genome Composition	p. 103
Reverse Biogeochemistry: Discovery of New Ecological Processes	p. 104
Environmental Reductionism: New Details About Recognized Processes	p. 106
Comparative Genomics and Metagenomics	p. 107
Future Directions	p. 122
Summary	p. 125
Acknowledgments	p. 125
References	p. 125
Photoheterotrophic Marine Prokaryotes	p. 131
Introduction	p. 131
Facultative Photoheterotrophy by Unicellular Cyanobacteria	p. 132
Cyanobacteria as Facultative Heterotrophs	p. 132
Uptake of Urea and DMSP	p. 133
Uptake of Nucleosides and Amino Acids	p. 134
Field Studies Using Light and Dark Incubations	p. 135
Implications of Facultative Photoheterotrophy by Cyanobacteria	p. 138
Marine AAnP Bacteria: Habitats and Diversity	p. 139
Rediscovery of the Marine AAnP Bacteria	p. 139
Diversity of AAnP Bacteria	p. 139
Physiology of AAnP Bacteria	p. 140
AAnP Bacterial Abundance and Ecological Significance	p. 142
Proteorhodopsin-Containing Prokaryotes	p. 143
Proteorhodopsin Genotypes and Taxonomic Distributions	p. 144
Proteorhodopsin Spectral Tuning	p. 145
Proteorhodopsin-Containing Prokaryotes: Abundance and Activity	p. 146
Proteorhodopsin-Containing Prokaryotes: Ecological Significance	p. 150
Summary	p. 151
References	p. 151
Ecology and Diversity of Picoeukaryotes	p. 159
Introduction	p. 159
Functional Roles, Classification, and Biological Traits	p. 162
Photoautotrophs	p. 163
Heterotrophs and Alternative Lifestyles	p. 170
Environmental Diversity and Molecular Phylogenetics	p. 172
Diversity of Uncultured Populations	p. 174
Methodological Issues for envPCR Studies	p. 178
Distribution, Abundance, and Activities	p. 179
Methods for Quantifying Mixed Assemblages	p. 180
Distribution, Abundance, and Activity of Mixed Picophytoplankton Assemblages	p. 182
Quantifying Specific Picoeukaryote Populations	p. 186
Methodological Challenges to Quantifying Specific Populations and Resolving Dynamics	p. 190
Mortality, Contributions to Microbial Food Webs, and Microbial Interactions	p. 191
Genomic Approaches to Picoeukaryote Ecology	p. 193
Integration of Picoeukaryotes to the Microbial Food Web: Research Directions	p. 194
Summary	p. 195
Acknowledgments	p. 196
References	p. 196
Organic Matter-Bacteria Interactions in Seawater	p. 207
Introduction	p. 207
Organic Matter Inventory and Fluxes	p. 208
DOM-Bacteria Interactions	p. 211
Labile Low-Molecular Weight (LMW) DOM	p. 211
Extracellular Hydrolytic Enzymes	p. 215
Polymeric DOM-Protein as a Model	p. 217
Refractory DOM	p. 220
POM-Bacteria Interactions	p. 223
POM Continuum	p. 223
POM Fluxes	p. 223
POM-Mineral Interactions	p. 229
Bacterial Community Structure and Utilization of Organic Matter	p. 230
Future Challenges	p. 231
Summary	p. 232
References	p. 232
Physiological Structure and Single-Cell Activity in Marine Bacterioplankton	p. 243
Introduction	p. 243
Distribution of Physiological States in Bacterioplankton Assemblages	p. 245
The Concept of "Physiological Structure" of Bacterioplankton Assemblages	p. 245
Starvation, Dormancy, and Viability in Marine Bacterioplankton	p. 246
Describing the Physiological Structure of Bacterioplankton	p. 250
Single-Cell Properties and Methodological Approaches	p. 250
Operational Categories of Single-Cell Activity	p. 259
Regulation of Physiological Structure of Marine Bacterioplankton	p. 260
Factors Influencing Physiological State of Bacterial Cells in Marine Ecosystems	p. 261
Factors Influencing Loss and Persistence of Physiological Fractions	p. 263
Distribution of Single-Cell Characteristics in Marine Bacterioplankton Assemblages	p. 265
Distribution of Single-Cell Activity and Physiological States in Marine Bacterioplankton	p. 265
Simultaneous Determination of Several Aspects of Single-Cell Activity and Physiology	p. 270
Patterns in Distribution of Single-Cell Activity and Physiology Along Marine Gradients	p. 271
Distribution of Activity and Growth Among Bacterial Size Classes	p. 273
Distribution of Activity Across and Within Major Phylogenetic Groups	p. 274
Dynamics of Single-Cell Activity and Physiological States	p. 276
Ecological Implications of Patterns in Bacterioplankton Single-Cell Activity	p. 279
Community Versus Individual Cell Growth and Metabolic Rates	p. 280
Linking the Distribution of Single-Cell Parameters and the Bulk Assemblage Response	p. 282
Ecological Role of Different Physiological Fractions	p. 283
Concluding Remarks	p. 284
Summary	p. 285
Acknowledgments	p. 285
References	p. 285
Heterotrophic Bacterial Respiration	p. 299
Introduction	p. 299
Measurement of Bacterial Respiration and Production	p. 301
Routine Measurement Techniques for Bacterial Respiration and Their Limitations	p. 301
Routine Measurement Techniques for Bacterial Production and Their Limitations	p. 304
Magnitude and Variability of Bacterial Respiration	p. 304
Temporal Variability	p. 308
Spatial Variability	p. 309
Relationship Between Bacterial Respiration and Environmental and Ecological Factors	p. 311
Bacterial Respiration as a Proportion of Community Respiration	p. 315
Predicting Bacterial Respiration	p. 317
Comparison Between Measurements and Predictions of Bacterial Respiration	p. 319
Magnitude of Bacterial Respiration in Relation to Primary Production	p. 321
Bacterial Respiration in a Changing Environment	p. 324
Summary	p. 326
Acknowledgments	p. 327
References	p. 327
Resource Control of Bacterial Dynamics in the Sea	p. 335
Introduction	p. 335
Growth in the Sea	p. 336
Growth and Nutrient Uptake Kinetics	p. 339
Approaches to Understanding Resource Control of Growth	p. 343
Comparative Approaches	p. 343
Experimental Approaches for Defining Limitation of Bacterial Growth	p. 349
Limitation by Dissolved Organic Matter	p. 351
Bacterial Growth on Bulk DOM Pools	p. 353
Limitation by Specific DOM Compounds	p. 354
Limitation by Inorganic Nutrients	p. 361
Nitrogen	p. 361
Phosphorus	p. 364
Trace Nutrients	p. 365
Temperature-DOM Interactions	p. 366
Light	p. 368
Resource Control of Specific Bacterial Populations in the Sea	p. 369
Summary	p. 371
Acknowledgments	p. 371
References	p. 371
Protistan Grazing on Marine Bacterioplankton	p. 383
Introduction	p. 383
New Insights into Phylogenetic Organization	p. 386
Functional Size Classes of Protists	p. 390
Natural Assemblages of Marine Heterotrophic Nanoflagellates	p. 391
Functional Ecology of Bacterivorous Flagellates	p. 394
Living in a Dilute Environment	p. 394
Using Culture Experiments to Infer the Ecological Role of HNF	p. 397
Impact of Protistan Bacterivory on Marine Bacterioplankton	p. 401
Search for the Perfect Method to Quantify Protistan Bacterivory	p. 401
Rates of Protistan Bacterivory in the Sea	p. 403
Balance of Bacterial Production and Protistan Grazing	p. 404
Bottom-Up Versus Top-Down Control of Bacteria and Bacterivorous Protists	p. 405
Ecological Functions of Bacterial Grazers	p. 406
Grazing as a Shaping Force of Bacterial Assemblages	p. 408
Bacterial Cell Size Determines Vulnerability Towards Grazers	p. 408
Other Antipredator Traits of Prokaryotes	p. 411
Grazing-Mediated Changes in Bacterial Community Composition	p. 414
Molecular Tools for Protistan Ecology	p. 414
Culturing Bias and Molecular Approaches	p. 414
Global Distribution and Diversity of Marine Protists	p. 420
Linking Diversity and Function for Uncultured Heterotrophic Flagellates	p. 422
Summary	p. 423
Acknowledgments	p. 424
References	p. 424
Marine Viruses: Community Dynamics, Diversity and Impact on Microbial Processes	p. 443
Introduction	p. 443
Viruses and the Marine Microbial Food Web	p. 444
Direct Counts and Viral Numbers	p. 444
Viral Production and Decay Rates	p. 447
Viral Decay and Rates of Production in Pelagic Systems	p. 447
Measurements of Viral Production in Marine Sediments	p. 449
General Rates of Viral Production	p. 449
Role of Viruses in Biogeochemical Cycling	p. 450
Impact of Viruses on Bacterial Diversity and Community Dynamics	p. 452
Marine Viral Diversity	p. 457
Methods for Examining Marine Viral Diversity	p. 457
Culture-Based Studies of Viral Diversity	p. 458
The Need for Culture-Independent Methods	p. 459
Culture-Independent Studies of Viral Diversity Using Transmission Electron Microscopy	p. 460
Whole-Genome Profiling of Viral Communities Based on Genome Size	p. 461
Studies of Viral Diversity Using Signature Genes	p. 461
Metagenomic Studies of Viral Diversity	p. 462
A Vision for the Future	p. 466
Summary	p. 467
References	p. 468
Molecular Ecological Aspects of Nitrogen Fixation in the Marine Environment	p. 481
Introduction	p. 481
Chemistry, Biochemistry, and Genetics of N[subscript 2] Fixation	p. 482
Genetics and Enzymology	p. 483
Evolution of N[subscript 2] Fixation	p. 485
Phylogeny of Nitrogenase	p. 487
Genomics of N[subscript 2] Fixation	p. 487
Diversity of N[subscript 2]-Fixing Microorganisms	p. 489
Regulation in Diazotrophs	p. 489
Methods for Assessing Diazotroph Diversity, Gene Expression, and N[subscript 2] Fixation Activity	p. 490
Ecophysiological Aspects of N[subscript 2] Fixation	p. 494
Ecology of Diazotrophs in the Open Ocean	p. 499
Estuarine and Coastal Waters	p. 505
Benthic Habitats, Including Microbial Mats and Reefs	p. 506
Deep Water and Hydrothermal Vents	p. 507
Summary	p. 508
Acknowledgments	p. 509
References	p. 509
Nitrogen Cycling in Sediments	p. 527
Introduction	p. 527
Inputs	p. 531
Transformations	p. 532
Microbes and Microbial Processes	p. 532
Processes Involving Mn and Fe	p. 548
Nitrogen Budgets	p. 550
Benthic Budgets	p. 550
Oceanic Budgets	p. 552
Summary	p. 554
References	p. 555
Index	p. 569
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