Processes in microbial ecology:
Gespeichert in:
| 1. Verfasser: | |
|---|---|
| Format: | Buch |
| Sprache: | German |
| Veröffentlicht: |
Oxford [u.a.]
Oxford University Press
2012
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| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | XIII, 312 Seiten Illustrationen, Diagramme |
| ISBN: | 9780199586929 9780199586936 |
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Datensatz im Suchindex
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|---|---|
| adam_text | Processes in Microbial
Ecology
David L Kirchman
School of Marine Science and Policy
University of Delaware, USA
OXFORD
UNIVERSITY PRESS
Table of Contents
Chapter 1 Introduction
What is a microbe? 1
Why study microbial ecology? 1
Microbes cause diseases of macroscopic organisms, including humans 2
Much of our food depends on microbes 3
Microbes degrade and detoxify pollutants 4
Microbes can be useful model systems for exploring general principles
in ecology and evolution 5
Some microbes are examples of early life on earth and perhaps of life on
other planets 6
Microbes mediate many biogeochemical processes that affect global climate 6
Microbes are everywhere, doing nearly everything 8
How do we study microbes in nature? 10
The three kingdoms of life: Bacteria, Archaea, and Eukarya 12
Functional groups of microbes 15
Autotroph versus heterotroph 16
Phototroph versus chemotroph 16
Sources of background information 16
Chapter 2 Elements, biochemicals, and structures of microbes 19
Elemental composition of microbes 19
Elemental ratios in biogeochemical studies 21
C:N and C:P ratios for various microbes 22
Biochemical composition of bacteria 23
Biochemical composition of eukaryotic microbes 24
Explaining elemental ratios 25
Architecture of a microbial cell 26
Membranes of microbes and active transport 26
Cell walls in prokaryotes and eukaryotes 27
Components of microbial cells as biomarkers 29
viii TABLE OF CONTENTS
Extracellular structures 31
Extracellular polymers of microbes 31
Flagella, cilia, fimbriae, and pili 32
Chapter 3 Physical-chemical environment of microbes 35
Water 35
Temperature 36
The effect of temperature on reaction rates 37
pH 39
Salt and osmotic balance 40
Oxygen and redox potential 41
Light 42
Pressure 43
The consequences of being small 44
Microbial life in natural aquatic habitats 46
Motility and taxis 47
Submicron- and micron-scale patchiness in aqueous environments 48
Microbial life in soils 49
Water content of soils 49
Interactions between temperature and water content in soils 50
The biofilm environment 51
Chapter 4 Microbial primary production and phototrophy 55
Basics of primary production and photosynthesis 55
Light and algal pigments 56
Transport of inorganic carbon 57
The carbon dioxide-fixing enzyme 59
Primary production, gross production, and net production 61
Primary production by terrestrial higher plants and aquatic microbes 63
The spring bloom and controls of phytoplankton growth 64
Major groups of bloom-forming phytoplankton 66
Diatoms 67
Coccolithophorids and the biological pump 67
Phaeocystis and dimethylsulfide 68
Diazotrophic filamentous cyanobacteria 69
After the bloom: picoplankton and nanoplankton 71
Competition for limiting nutrients 71
Primary production by coccoid cyanobacteria 73
Photoheterotrophy in the oceans 74
Uptake of organic material by algae 75
Aerobic anoxygenic phototrophic bacteria 75
Rhodopsin in photoheterotrophic bacteria 76
Ecological and biogeochemical impacts of photoheterotrophy 77
TABLE OF CONTENTS ix
Chapter 5 Degradation of organic material 79
Mineralization of organic material in various ecosystems 80
Who does most of the respiration on the planet? 81
Slow and fast carbon cycling pathways 83
Chemical characterization of detrital organic material 84
Dissolved organic material 85
Detrital food webs 86
DOM and the microbial loop 88
Hydrolysis of high molecular weight organic compounds 91
Lignin degradation 93
Uptake of low molecular weight organic compounds: turnover versus reservoir size 93
Chemical composition and organic material degradation 94
Release of inorganic nutrients and its control 96
Photo-oxidation of organic material 96
Refractory organic matter 97
Chapter 6 Microbial growth, biomass production, and controls 99
Are bacteria alive or dead? 99
Activity state of bacteria in soils and sediments 101
Activity state of soil fungi 101
Microbial growth and biomass production 102
Growth of pure cultures in the lab: batch cultures 102
Growth of pure cultures in the lab: continuous cultures 103
Measuring growth and biomass production in nature 104
Bacterial biomass production in aquatic environments 105
Bacterial growth rates in aquatic environments 107
Growth rates of bacteria and fungi in soils 108
What sets biomass production and growth by microbes in nature? 109
Temperature effects on growth and carbon cycling 109
Temperature effects on fungi versus bacteria in soils 111
Limitation by organic carbon 111
Limitation by inorganic nutrients 113
Co-limitation and interactions between controlling factors 114
Competition and chemical communication between organisms 115
Chapter 7 Predation and protists 117
Bacterivory and herbivory in aquatic habitats 118
Grazers of bacteria and fungi in soils and sediments 120
Grazing mechanism for protists 121
Factors affecting grazing 122
Prey number and predator-prey cycles 123
Size relationships of predator and prey 125
Chemical recognition and composition 126
X TABLE OF CONTENTS
Defenses against grazing 128
Effect of grazing on prey growth 129
Grazing by ciliates and dinoflagellates 129
Ciliates as herbivores in aquatic ecosystems 129
Ciliates in soils and sediments 130
Heterotrophic dinoflagellates 131
Fluxes from microbial food webs to higher trophic levels 132
Mixotrophic protists and endosymbiosis 133
Phagotrophy, endosymbiosis, and algal evolution 135
Chapter 8 Ecology of viruses 137
What are viruses? 137
Viral replication 138
Temperate viruses in nature 139
Contact between host and virus at the molecular scale 140
The number of viruses in natural environments 141
Counting viruses by the plaque assay 142
Counting viruses by microscopy 142
Variation in viral abundance in nature 144
Mortality of bacteria due to viruses 146
Percentage of infected cells 146
The viral reduction method 146
Contribution of viruses versus grazers to bacterial mortality 147
Viral production and turnover 148
Viral decay and loss 148
Viruses of phytoplankton 149
Viruses are not grazers 150
Viral shunt and DOM production 151
Population dynamics of a virus and its host 151
Genetic exchange mediated by viruses 152
Chapter 9 Community structure of microbes in natural environments 157
Taxonomy and phylogeny via genes 157
Introduction to 16S rRNA-based methods 158
The species problem 159
Diversity of bacterial communities 160
The paradox of the plankton 162
Differences between cultivated and uncultivated microbes 163
Types of bacteria in soils, freshwaters, and the oceans 164
Archaea in non-extreme environments 166
Everything, everywhere? 167
What controls diversity levels and bacterial community structure? 168
Temperature, salinity, and pH 168
Moisture and soil microbial communities 169
TABLE OF CONTENTS xi
Organic material and primary production 170
Predation and viral lysis 171
Problems with 16S rRNA as a taxonomic and phylogenetic tool 171
Community structure of protists and other eukaryotic microbes 173
Types of protists and other eukaryotic microbes in nature 173
Relevance of community structure to understanding processes 175
Chapter 10 Genomes and metagenomes of microbes and viruses 177
What are genomics and environmental genomics? 177
Turning genomic sequences into genomic information 178
Lessons from cultivated microbes 179
Similar rRNA genes, dissimilar genomes 179
Genome size 180
Organization of eukaryotic versus prokaryotic genomes 181
Growth rates and genomics 182
Chromosomes, plasmids, and replicons 183
Lateral gene transfer 184
Genomes from uncultivated microbes: metagenomics 185
Metagenomic approaches 186
The proteorhodopsin story and others 187
Metagenomics of a simple community in acid mine drainage 188
Useful compounds from metagenomics and activity screening 188
Metatranscriptomicsand metaproteomics 189
Proteomics and metaproteomics 191
Metagenomics of viruses 191
RNA viruses 193
Chapter 11 Processes in anoxic environments 195
Introduction to anaerobic respiration 195
The order of electron acceptors 197
Oxidation of organic carbon by various electron acceptors 199
Limited by concentrations and supply 199
Effect of chemical form 200
The anaerobic food chain 201
Fermentation 202
Interspecies hydrogen transfer and syntrophy 203
Sulfate reduction 204
Electron donors for sulfate reduction 205
Sulfur oxidation and the rest of the sulfur cycle 207
Non-phototrophic sulfur oxidation 208
Sulfide oxidation by anoxygenic photosynthesis 209
The carbon source for sulfur oxidizers 210
Methane and methanogenesis 210
Methanotrophy 212
xii TABLE OF CONTENTS
Aerobic methane degradation 212
Anaerobic methane oxidation 213
Anaerobic eukaryotes 214
Chapter 12 The nitrogen cycle 217
Nitrogen fixation 218
Nitrogenase, the nitrogen-fixing enzyme 218
Solving the oxygen problem 219
N2 fixation in nature 220
Limitation of N2 fixation 221
Ammonium assimilation, regeneration, and fluxes 221
Ammonium release in anoxic systems 223
Ammonium uptake versus excretion, immobilization versus mobilization 223
Ammonia oxidation, nitrate production, and nitrification 224
Aerobic ammonia oxidation by bacteria 225
Archaeal ammonia oxidation 226
Controls of aerobic ammonia oxidation 228
Nitrite oxidation and the second step in nitrification 229
Anaerobic ammonia oxidation 229
Dissimilatory nitrate reduction and denitrification 230
Dissimilatory nitrate reduction to ammonium 231
Denitrification versus anaerobic ammonium oxidation 232
Sources and sinks of nitrous oxide 233
Balancing N loss and N2 fixation 234
Chapter 13 Introduction to geomicrobiology 237
Cell surface charge, metal sorption, and microbial attachment 237
Metal sorption 238
Iron uptake mediated by siderophores and other metal ligands 239
Attachment of microbes to surfaces 241
Biomineralization by microbes 241
Carbonate minerals 242
Phosphorus minerals 244
Iron mineral formation by non-enzymatic processes 245
Magnetite and magnetotactic bacteria 246
Manganese and iron-oxidizing bacteria 248
Iron oxidation 248
Manganese-oxidizing bacteria 250
Weathering and mineral dissolution by microbes 251
Dissolution by acid and base production 251
Dissolution by low and high molecular weight chelators 252
Geomicrobiology of fossil fuels 253
TABLE OF CONTENTS xiii
Chapter 14 Symbiosis and microbes 257
Microbial residents of vertebrates 259
Microbial symbioses with insects 261
Microbial symbionts in termites 261
Aphids-fiuchnera symbiosis 262
Symbiotic relationship between ants and fungi 263
Symbiotic microbes in marine invertebrates 265
Endosymbionts in Riftia and other sulfide-oxidizing symbionts 266
Bioluminescent symbionts in the oceans 269
Microbe-plant symbioses 271
Diazotrophic bacteria and plant symbioses 271
Fungi-plant symbioses 273
Concluding remarks 275
References 277
Index 303
|
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| spelling | Kirchman, David L. Verfasser aut Processes in microbial ecology David L. Kirchman Oxford [u.a.] Oxford University Press 2012 XIII, 312 Seiten Illustrationen, Diagramme txt rdacontent n rdamedia nc rdacarrier Mikrobiologie (DE-588)4316357-9 gnd rswk-swf Mikroorganismus (DE-588)4039226-0 gnd rswk-swf Ökologie (DE-588)4043207-5 gnd rswk-swf Mikroorganismus (DE-588)4039226-0 s Ökologie (DE-588)4043207-5 s DE-604 Mikrobiologie (DE-588)4316357-9 s 1\p DE-604 HEBIS Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=022518327&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis 1\p cgwrk 20201028 DE-101 https://d-nb.info/provenance/plan#cgwrk |
| spellingShingle | Kirchman, David L. Processes in microbial ecology Mikrobiologie (DE-588)4316357-9 gnd Mikroorganismus (DE-588)4039226-0 gnd Ökologie (DE-588)4043207-5 gnd |
| subject_GND | (DE-588)4316357-9 (DE-588)4039226-0 (DE-588)4043207-5 |
| title | Processes in microbial ecology |
| title_auth | Processes in microbial ecology |
| title_exact_search | Processes in microbial ecology |
| title_full | Processes in microbial ecology David L. Kirchman |
| title_fullStr | Processes in microbial ecology David L. Kirchman |
| title_full_unstemmed | Processes in microbial ecology David L. Kirchman |
| title_short | Processes in microbial ecology |
| title_sort | processes in microbial ecology |
| topic | Mikrobiologie (DE-588)4316357-9 gnd Mikroorganismus (DE-588)4039226-0 gnd Ökologie (DE-588)4043207-5 gnd |
| topic_facet | Mikrobiologie Mikroorganismus Ökologie |
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