آشنایی با ژئومیکروبیولوژی ۲۰۰۹
Introduction to Geomicrobiology 2009

1. Preface

1 Microbial properties and diversity

1.1 Classification of life

1.2 Physical properties of microorganisms

1.2.1 Prokaryotes

1.2.2 Eukaryotes

1.3 Requirements for growth

1.3.1 Physical requirements

1.3.2 Chemical requirements

1.3.3 Growth rates

1.4 Microbial diversity

1.5 Life in extreme environments

1.5.1 Hydrothermal systems

1.5.2 Polar environments viable population is available to seed the global

1.5.3 Acid environments

1.5.4 Hypersaline and alkaline environments

1.5.5 Deep-subsurface environments

1.5.6 Life on other planets

1.5.7 Panspermia

1.6 Summary

2 Microbial metabolism

2.1 Bioenergetics

2.1.1 Enzymes

2.1.2 Oxidation-reduction

2.1.3 ATP generation

2.1.4 Chemiosmosis

2.2 Photosynthesis

2.2.1 Pigments

2.2.2 The light reactions – anoxygenic photosynthesis

2.2.3 Classification of anoxygenic photosynthetic bacteria

2.2.4 The light reactions – oxygenic photosynthesis

2.2.5 The dark reactions

2.2.6 Nitrogen fixation

2.3 Catabolic processes

2.3.1 Glycolysis and fermentation

2.3.2 Respiration

2.4 Chemoheterotrophic pathways

2.4.1 Aerobic respiration

2.4.2 Dissimilatory nitrate reduction

2.4.3 Dissimilatory manganese reduction

2.4.4 Dissimilatory iron reduction

2.4.5 Trace metal and metalloid reductions

2.4.6 Dissimilatory sulfate reduction

2.4.7 Methanogenesis and homoacetogenesis

2.5 Chemolithoautotrophic pathways

2.5.1 Hydrogen oxidizers

2.5.2 Homoacetogens and methanogens

2.5.3 Methylotrophs

2.5.4 Sulfur oxidizers

2.5.5 Iron oxidizers

2.5.6 Manganese oxidizers

2.5.7 Nitrogen oxidizers

3 Cell surface reactivity and metal sorption

3.1 The cell envelope

3.1.1 Bacterial cell walls

3.1.2 Bacterial surface layers

3.1.3 Archaeal cell walls

3.1.4 Eukaryotic cell walls

3.2 Microbial surface charge

3.2.1 Acid–base chemistry of microbial surfaces

3.2.2 Electrophoretic mobility

3.2.3 Chemical equilibrium models

3.3 Passive metal adsorption

3.3.1 Metal adsorption to bacteria

3.3.2 Metal adsorption to eukaryotes

3.3.3 Metal cation partitioning

3.3.4 Competition with anions

3.4 Active metal adsorption

3.4.1 Surface stability requirements

3.4.2 Metal binding to microbial exudates

3.5 Bacterial metal sorption models

3.5.1 Kd coefficients

3.5.2 Freundlich isotherms

3.5.3 Langmuir isotherms

3.5.4 Surface complexation

3.5.5 Does a generalized sorption model exist?

3.6 The microbial role in contaminant mobility

3.6.1 Microbial sorption to solid surfaces

3.6.2 Microbial transport through porous media

3.7 Industrial applications based on microbial surface reactivity

3.7.1 Bioremediation

3.7.2 Biorecovery

3.8 Summary

4 Biomineralization

4.1 Biologically induced mineralization

4.1.1 Mineral nucleation and growth

4.1.2 Iron hydroxides

4.1.3 Magnetite

4.1.4 Manganese oxides

4.1.5 Clays

4.1.6 Amorphous silica

4.1.7 Carbonates

4.1.8 Phosphates

4.1.9 Sulfates

4.1.10 Sulfide minerals

4.2 Biologically controlled mineralization

4.2.1 Magnetite

4.2.2 Greigite

4.2.3 Amorphous silica

4.2.4 Calcite

4.3 Fossilization

4.3.1 Silicification

4.3.2 Other authigenic minerals

4.4 Summary

5 Microbial weathering

5.1 Mineral dissolution

5.1.1 Reactivity at mineral surfaces

5.1.2 Microbial colonization and organic reactions

5.1.3 Silicate weathering

5.1.4 Carbonate weathering

5.1.5 Soil formation

5.1.6 W eathering and global climate

5.2 Sulfide oxidation

5.2.1 Pyrite oxidation mechanisms

5.2.2 Biological role in pyrite oxidation

5.2.3 Bioleaching

5.2.4 Biooxidation of refractory gold

5.3 Microbial corrosion

5.3.1 Chemolithoautotrophs

5.3.2 Chemoheterotrophs

5.3.3 Fungi

5.4 Summary

6 Microbial zonation

6.1 Microbial mats

6.1.1 Mat development

6.1.2 Photosynthetic mats

6.1.3 Chemolithoautotrophic mats

6.1.4 Biosedimentary structures

6.2 Marine sediments

6.2.1 Organic sedimentation

6.2.2 An overview of sediment diagenesis

6.2.3 Oxic sediments

6.2.4 Suboxic sediments

6.2.5 Anoxic sediments

6.2.6 Preservation of organic carbon Preservation of organic carbon

6.2.7 Diagenetic mineralization

6.2.8 Sediment hydrogen concentrations

6.2.9 Problems with the biogeochemical zone scheme

6.3 Summary

7 Early microbial life

7.1 The prebiotic Earth

7.1.1 The Hadean environment

7.1.2 Origins of life

7.1.3 Mineral templates

7.2 The first cellular life forms

7.2.1 The chemolithoautotrophs

7.2.2 Deepest-branching Bacteria and Archaea

7.2.3 The fermenters and initial respirers

7.3 Evolution of photosynthesis

7.3.1 Early phototrophs

7.3.2 Photosynthetic expansion

7.3.3 The cyanobacteria

7.4 Metabolic diversification

7.4.1 Obligately anaerobic respirers

7.4.2 Continental platforms as habitats

7.4.3 Aerobic respiratory pathways

7.5 Earth’s oxygenation

7.5.1 The changing Proterozoic environment

7.5.2 Eukaryote evolution

7.6 Summary

161. References

162. Index