Microbial Ecology of the Oceans [NOOK Book]

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