Microbial ecology of the oceans
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| Format: | Buch |
| Sprache: | English |
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Wiley
2008
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| 245 | 1 | 0 | |a Microbial ecology of the oceans |c David L. Kirchman |
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Datensatz im Suchindex
| _version_ | 1819635180934004736 |
|---|---|
| adam_text | Titel: Microbial ecology of the oceans
Autor: Kirchman, David L.
Jahr: 2008
CONTENTS
PREFACE xv
CONTRIBUTORS xvii
1 INTRODUCTION AND OVERVIEW 1
David L. Kirchman
Eukaryotic Phytoplankton and Cyanobacteria 3
Photoheterotrophic Bacteria 5
Dissolved Organic Material 7
Heterotrophic Bacteria 10
Marine Archaea 13
Heterotrophic Protists 14
Nanoflagellates (2-20 |xm) 14
Microzooplanktonic Protists (20-200 xxri) 16
Dinoflagellates 16
Marine Fungi 16
Marine Viruses 17
N2 Fixers 18
Nitrifiers and Other Chemolithotrophs 19
Denitrifiers 20
Concluding Remarks 21
Summary 22
Acknowledgments 22
References 23
v
t,
VI CONTENTS
2 UNDERSTANDING ROLES OF MICROBES IN MARINE
PELAGIC FOOD WEBS: A BRIEF HISTORY 27
Evelyn Sherr and Barry Sherr
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
3 BACTERIAL AND ARCHAEAL COMMUNITY
STRUCTURE AND ITS PATTERNS 45
Jed A. Fuhrman and Ake Hagstrom
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
SARI 16 Cluster 59
SAR202 59
Marine Group A 59
Marine Group B 59
Betaproteobacteria 59
Marine Archaea 60
Bacterioplankton Diversity 63
Species Concept 63
CONTENTS Vii
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
4 GENOMICS AND METAGENOMICS OF MARINE
PROKARYOTES 91
Mary Ann Moran
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
Viii CONTENTS
5 PHOTOHETEROTROPHIC MARINE PROKARYOTES 131
Oded Beja and Marcelino T. Suzuki
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
6 ECOLOGY AND DIVERSITY OF PICOEUKARYOTES 159
Alexandra Z. Worden and Fabrice Not
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
CONTENTS ix
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
7 ORGANIC MATTER-BACTERIA INTERACTIONS
IN SEAWATER 207
Toshi Nagata
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
8 PHYSIOLOGICAL STRUCTURE AND SINGLE-CELL
ACTIVITY IN MARINE BACTERIOPLANKTON 243
Paul A. del Giorgio and Josep M. Gasol
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
X CONTENTS
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
9 HETEROTROPHIC BACTERIAL RESPIRATION 299
Carol Robinson
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
CONTENTS Xi
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
10 RESOURCE CONTROL OF BACTERIAL DYNAMICS
IN THE SEA 335
Matthew J. Church
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
Xii CONTENTS
11 PROTISTAN GRAZING ON MARINE BACTERIOPLANKTON 383
Klaus Jiirgens and Ramon Massana
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 413
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
12 MARINE VIRUSES: COMMUNITY DYNAMICS,
DIVERSITY AND IMPACT ON
MICROBIAL PROCESSES 443
Mya Breitbart, Mathias Middelboe, and Forest Rohwer
Introduction 443
Viruses and the Marine Microbial Food Web 444
Direct Counts and Viral Numbers 444
CONTENTS Xiii
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
13 MOLECULAR ECOLOGICAL ASPECTS OF NITROGEN
FIXATION IN THE MARINE ENVIRONMENT 481
Jonathan P. Zehr and Hans W. Paerl
Introduction 481
Chemistry, Biochemistry, and Genetics of N2 Fixation 482
Genetics and Enzymology 483
Evolution of N2 Fixation 485
Phylogeny of Nitrogenase 487
Genomics of N2 Fixation 487
Diversity of N2-Fixing Microorganisms 489
Regulation in Diazotrophs 489
Methods for Assessing Diazotroph Diversity,
Gene Expression, and N2 Fixation Activity 490
Ecophysiological Aspects of N2 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
XIV CONTENTS
14 NITROGEN CYCLING IN SEDIMENTS 527
Bo Thamdrup and Tage Dalsgaard
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
|
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| id | DE-604.BV025512260 |
| illustrated | Illustrated |
| indexdate | 2024-12-23T23:52:31Z |
| institution | BVB |
| isbn | 047004344X 9780470043448 |
| language | English |
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| spellingShingle | Kirchman, David L. Microbial ecology of the oceans Meer (DE-588)4038301-5 gnd Mikrobiologie (DE-588)4316357-9 gnd Bakterien (DE-588)4004296-0 gnd Mikroorganismus (DE-588)4039226-0 gnd Meeresbiologie (DE-588)4169246-9 gnd Meeresökologie (DE-588)4195671-0 gnd |
| subject_GND | (DE-588)4038301-5 (DE-588)4316357-9 (DE-588)4004296-0 (DE-588)4039226-0 (DE-588)4169246-9 (DE-588)4195671-0 |
| title | Microbial ecology of the oceans |
| title_auth | Microbial ecology of the oceans |
| title_exact_search | Microbial ecology of the oceans |
| title_full | Microbial ecology of the oceans David L. Kirchman |
| title_fullStr | Microbial ecology of the oceans David L. Kirchman |
| title_full_unstemmed | Microbial ecology of the oceans David L. Kirchman |
| title_short | Microbial ecology of the oceans |
| title_sort | microbial ecology of the oceans |
| topic | Meer (DE-588)4038301-5 gnd Mikrobiologie (DE-588)4316357-9 gnd Bakterien (DE-588)4004296-0 gnd Mikroorganismus (DE-588)4039226-0 gnd Meeresbiologie (DE-588)4169246-9 gnd Meeresökologie (DE-588)4195671-0 gnd |
| topic_facet | Meer Mikrobiologie Bakterien Mikroorganismus Meeresbiologie Meeresökologie |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=020122257&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| work_keys_str_mv | AT kirchmandavidl microbialecologyoftheoceans |