Microbial ecology of the oceans:
Gespeichert in:
| Weitere Verfasser: | , |
|---|---|
| Format: | Buch |
| Sprache: | English |
| Veröffentlicht: |
Hoboken, NJ
Wiley Blackwell
2018
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| Ausgabe: | Third edition |
| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis Klappentext |
| Beschreibung: | xvi, 507 Seiten, 40 ungezählte Seiten Tafeln Illustrationen, Diagramme |
| ISBN: | 9781119107187 |
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| 245 | 1 | 0 | |a Microbial ecology of the oceans |c edited by Josep M. Gasol (Instiut de Ciències del Mar, CSIC, Barcelona, Catalunya, Spain), David L. Kirchman (School of Marine Science and Policy, University of Delaware, USA) |
| 250 | |a Third edition | ||
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Datensatz im Suchindex
| _version_ | 1804178577633050624 |
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| adam_text | 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:
rRNA-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 Single-Cell Microbial Oceanography 24
1.4.2 Toward Understanding Cell-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
v
VI
CONTENTS
2 MARINE MICROBIAL DIVERSITY AS SEEN BY
HIGH-THROUGHPUT SEQUENCING 47
Carlos Pedros-A Ho, 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 Single-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,
Microbe-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
CONTENTS Vii
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 Cultivation-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 Single-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 Martinez-Garcia and Jarone Pinhassi
5.1 Introduction 149
5.2 Cultivation Approaches 153
5.3 Lessons Learned from Ecophysiological Response Experiments
with Cultivated B acteria 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
viii
CONTENTS
5.3.4 Phage-Host Model Systems in Cyanobacteria and
Heterotrophic Bacteria 168
5.3.5 Deep-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 Broad-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
OXYGEN-DEFICIENT WATER COLUMNS 231
Klaus JUrgens 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 Oxygen-Deficient Aquatic Systems 237
7.5 Physico-Chemical Profiles as Indicators of Biogeochemical Zones 240
7.6 General Considerations of Microbial Metabolism in ODWCs 243
CONTENTS
ix
7.7 Biogeochemical Cycles in Oxygen-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 27 3
7.11 References 273
8 THE OCEAN’S MICROSCALE: A MICROBES 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 Cell-to-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
Jennifer R. Brum and Matthew B. Sullivan
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
9.4.1 Estimating the Size of the Global Virome
9.4.2 Estimating Viral Richness
9.4.3 Marine Viral Community Structure and
Ecological Drivers
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
9.9.1 The Need to Capture Other Viral Types
9.9.2 Moving Beyond Upper-Ocean Waters
9.9.3 Making the Genes-to-Ecosy stems Leap to Evaluate
Processes
9.10 Summary
9.11 Acknowledgments
9.12 References
10 MICROBIAL PHYSIOLOGICAL ECOLOGY OF THE
MARINE PHOSPHORUS CYCLE
Sonya T. Dyhrman
10.1 Introduction
10.2 Methodological Advances and Challenges
10.3 Phosphorus Biogeochemistry
10.3.1 The Phosphorus Cycle
10.3.2 Sources and Sinks
10.3.3 Phosphorus Stoichiometry
10.4 Phosphorus in the Cell
10.4.1 Phosphorus Biochemicals
10.4.2 Phosphorus Redox State
10.4.3 Phosphorus Bond Classes
10.5 Microbial Biogeochemistry of Phosphorus Bond Types
10.5.1 Polyphosphate
10.5.2 Phosphoester
10.5.3 Phosphonate
CONTENTS
345
345
348
350
351
353
354
354
356
359
361
364
365
365
366
367
368
369
369
377
377
379
382
382
382
383
383
383
385
386
386
387
389
390
CONTENTS
xi
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 High-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 Trade-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
xii
CONTENTS
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
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.
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| id | DE-604.BV044976573 |
| illustrated | Illustrated |
| indexdate | 2024-07-10T08:06:11Z |
| institution | BVB |
| isbn | 9781119107187 |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-030369006 |
| oclc_num | 1029210758 |
| open_access_boolean | |
| owner | DE-11 DE-384 DE-703 |
| owner_facet | DE-11 DE-384 DE-703 |
| physical | xvi, 507 Seiten, 40 ungezählte Seiten Tafeln Illustrationen, Diagramme |
| publishDate | 2018 |
| publishDateSearch | 2018 |
| publishDateSort | 2018 |
| publisher | Wiley Blackwell |
| record_format | marc |
| spelling | Microbial ecology of the oceans edited by Josep M. Gasol (Instiut de Ciències del Mar, CSIC, Barcelona, Catalunya, Spain), David L. Kirchman (School of Marine Science and Policy, University of Delaware, USA) Third edition Hoboken, NJ Wiley Blackwell 2018 xvi, 507 Seiten, 40 ungezählte Seiten Tafeln Illustrationen, Diagramme txt rdacontent n rdamedia nc rdacarrier Meeresökologie (DE-588)4195671-0 gnd rswk-swf Mikrobiologie (DE-588)4316357-9 gnd rswk-swf Mikroorganismus (DE-588)4039226-0 gnd rswk-swf Meeresbiologie (DE-588)4169246-9 gnd rswk-swf Meer (DE-588)4038301-5 gnd rswk-swf Bakterien (DE-588)4004296-0 gnd rswk-swf Meeresökologie (DE-588)4195671-0 s Mikroorganismus (DE-588)4039226-0 s DE-604 Meeresbiologie (DE-588)4169246-9 s Mikrobiologie (DE-588)4316357-9 s 1\p DE-604 Bakterien (DE-588)4004296-0 s 2\p DE-604 Meer (DE-588)4038301-5 s 3\p DE-604 Gasol, Josep M. 1962- (DE-588)1154869466 edt Kirchman, David L. (DE-588)1159967180 edt Erscheint auch als Online-Ausgabe 978-1-119-10720-0 Digitalisierung UB Augsburg - ADAM Catalogue Enrichment application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=030369006&sequence=000003&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis Digitalisierung UB Augsburg - ADAM Catalogue Enrichment application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=030369006&sequence=000004&line_number=0002&func_code=DB_RECORDS&service_type=MEDIA Klappentext 1\p cgwrk 20201028 DE-101 https://d-nb.info/provenance/plan#cgwrk 2\p cgwrk 20201028 DE-101 https://d-nb.info/provenance/plan#cgwrk 3\p cgwrk 20201028 DE-101 https://d-nb.info/provenance/plan#cgwrk |
| spellingShingle | Microbial ecology of the oceans Meeresökologie (DE-588)4195671-0 gnd Mikrobiologie (DE-588)4316357-9 gnd Mikroorganismus (DE-588)4039226-0 gnd Meeresbiologie (DE-588)4169246-9 gnd Meer (DE-588)4038301-5 gnd Bakterien (DE-588)4004296-0 gnd |
| subject_GND | (DE-588)4195671-0 (DE-588)4316357-9 (DE-588)4039226-0 (DE-588)4169246-9 (DE-588)4038301-5 (DE-588)4004296-0 |
| 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 edited by Josep M. Gasol (Instiut de Ciències del Mar, CSIC, Barcelona, Catalunya, Spain), David L. Kirchman (School of Marine Science and Policy, University of Delaware, USA) |
| title_fullStr | Microbial ecology of the oceans edited by Josep M. Gasol (Instiut de Ciències del Mar, CSIC, Barcelona, Catalunya, Spain), David L. Kirchman (School of Marine Science and Policy, University of Delaware, USA) |
| title_full_unstemmed | Microbial ecology of the oceans edited by Josep M. Gasol (Instiut de Ciències del Mar, CSIC, Barcelona, Catalunya, Spain), David L. Kirchman (School of Marine Science and Policy, University of Delaware, USA) |
| title_short | Microbial ecology of the oceans |
| title_sort | microbial ecology of the oceans |
| topic | Meeresökologie (DE-588)4195671-0 gnd Mikrobiologie (DE-588)4316357-9 gnd Mikroorganismus (DE-588)4039226-0 gnd Meeresbiologie (DE-588)4169246-9 gnd Meer (DE-588)4038301-5 gnd Bakterien (DE-588)4004296-0 gnd |
| topic_facet | Meeresökologie Mikrobiologie Mikroorganismus Meeresbiologie Meer Bakterien |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=030369006&sequence=000003&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=030369006&sequence=000004&line_number=0002&func_code=DB_RECORDS&service_type=MEDIA |
| work_keys_str_mv | AT gasoljosepm microbialecologyoftheoceans AT kirchmandavidl microbialecologyoftheoceans |