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Index
Microbial Evolution under Extreme Conditions
Life in Extreme Environments
Title Page
Copyright Page
Preface
Table of Contents
Contributing authors
1 Extreme environments as model systems for the study of microbial evolution
1.1 Introduction
1.2 Extreme environments as model systems
1.3 What is known about microbial evolution?
1.3.1 Community diversity as a measure of evolution
1.3.2 Adaptive traits as a measure of evolution
1.4 Themes from extreme environments
1.5 Conclusions and open questions
References
2 Microbial evolution: the view from the acidophiles
2.1 Introduction
2.2 Horizontal gene transfer
2.3 The mobilome
2.4 Phages
2.5 Plasmids
2.6 Transposons
2.7 Evolution and ecology: long term studies of genetic variation
2.8 Future directions
Acknowledgments
References
3 Microbial Evolution in the Cryosphere
3.1 Overview
3.1.1 Cryospheric evironments
3.1.1.1 Seasonally frozen environments: sea ice, snow, and the active layer
3.1.1.2 Perennially frozen environments: glaciers, ice sheets, and permafrost
3.1.2 Modes of evolution
3.1.2.1 Darwinian Processes
3.1.2.2 Horizontal gene transfer
3.1.3 Adaptations to living with ice
3.2 Focus on sea ice
3.2.1 Sea ice characteristics
3.2.1.1 Physical properties shape the biological communities
3.2.1.2 Sea ice microbial communities
3.2.2 Evolutionary modes in sea ice
3.2.2.1 Horizontal gene transfer
3.3 Ongoing work and future directions
3.3.1 Field work and experimentation
3.3.2 ‘-omics’ in the cryosphere
3.3.3 Linking phenotype and genotype
Acknowledgments
References
4 Metabolic and taxonomic diversification in continental magmatic hydrothermal systems
4.1 Introduction
4.2 Geological drivers of geochemical variation in continental hydrothermal systems
4.3 Taxonomic and functional diversity in continental hydrothermal ecosystems
4.4 Application of phylogenetic approaches to map taxonomic and functional diversity on spatial geochemical landscapes
4.5 Molecular adaptation to high temperature
4.5.1 Lipids
4.5.2 Protein stability
4.5.3 Cytoplasmic osmolytes
4.5.4 Motility
4.6 Mechanisms of evolution in high temperature environments
4.7 Concluding remarks
References
5 Halophilic microorganisms and adaptation to life at high salt concentrations - evolutionary aspects
5.1 Phylogenetic and physiological diversity of halophilic microorganisms
5.2 What adaptations are necessary to become a halophile?
5.3 Is an acidic (meta)proteome indeed indicative for hatophily and high intracellular ionic concentrations?
5.4 Genetic variation and horizontal gene transfer in communities of halophilic Archaea
5.5Salinibacter: convergent evolution and the ‘salt-in’ strategy of haloadaptation
5.6 High intracellular K+ concentrations but no acidic proteome? The case of the Halanaerobiales
5.7 Different modes of haloadaptation in closely related Halorhodospira species
5.8 Final comments
Acknowledgments
References
6 The origin of extreme ionizing radiation resistance
6.1 Introduction and background
6.1.1 Ionizing radiation
6.1.2 Biological damage caused by electromagnetic radiations
6.1.3 Exposure to ionizing radiation selects for ionizing radiation resistant bacteria
6.1.4 The occurrence of extreme ionizing radiation resistance within the Bacteriaand Archaea
6.1.5 Natural sources of ionizing radiation
6.2 The existence of extreme ionizing radiation resistance is difficult to reconcile with the natural history of the Earth
6.3 Proposed explanations for the existence of ionizing radiation resistance
6.3.1 Panspermia: the exchange of bacteria between planets
6.3.2 Man-made sources of ionizing radiation are the source of extreme ionizing radiation resistant microorganisms
6.3.3 Exaptation
6.4 Conclusions
References
7 Current perspectives on microbial strategies for survival under extreme nutrient starvation: evolution and ecophysiology
7.1 Introduction
7.2 Carbon
7.3 Nitrogen
7.4 Phosphorus
7.5 Iron
7.6 Other micronutrients
7.7 Conclusions
References
8 Polyextremophiles
8.1 Introduction
8.2 Bacteria
8.2.1 Deinococcus radiodurans: Conan the bacterium
8.2.2 Chroococcidiopsis
8.3 Archaea
8.3.1 Halobacterium salinarum NRC-1: a model organism
8.4 Eukaryota
8.4.1 Cyanidiophyceae
8.4.2 Lichens
8.4.3 Tardigrades: nature’s toughest animal
8.5 Conclusion
References
9 Early life
References
10 Polyextremotolerance as the fungal answer to changing environments
10.1 Introduction
10.2 Extremes in nature
10.3 Anthropogenic extremes: indoor habitats
10.4 Coincidental opportunities: opportunistic infections
10.5 Conclusions: polyextremotolerance
Acknowledgments
References
11 Viral evolution at the limits
11.1 Introduction
11.2 Acidic hot springs and hypersaline environments
11.3 The deep sea
11.4 Polar environments
11.5 Viruses and their effects on host organisms and communities
11.6 Future perspectives
Acknowledgments
References
12 Evolutionary pressures and the establishment of endosymbiotic associations
12.1 Introduction
12.2 Diversity, evolution, and stability of endosymbiotic relationships
12.2.1 Diversity of endosymbionts and their physiological functions
12.2.2 Evolutionary routes to establish and maintain endosymbiosis
12.2.3 Stability and the age of endosymbioses
12.3 Genome evolution in endosymbiotic bacteria
12.3.1 Reductive genome evolution in endosymbionts
12.3.2 Evolution toward an organelle and beyond
12.4 Evolution of the host genome as shaped by endosymbiosis
12.4.1 Complementarity of host and endosymbiont metabolic abilities
12.4.2 Acquisition of symbiotic potential
12.4.2.1 Acquisition of symbiotic potential through HGT
12.4.2.2 Acquisition of symbiotic potential through gene duplications
12.4.2.3 Acquisition of symbiotic potential through de novo gene evolution
12.4.3 Redefinition of immune functions
12.5 Conclusions and future directions
Acknowledgments
References
13 Rates of evolution under extreme and mesophilic conditions
13.1 Overview
13.2 How do we estimate rates of genetic change?
13.2.1 Relative rate estimation
13.2.2 Absolute rate estimation
13.2.2.1 The genetic distances problem
13.2.2.2 The calibration points problem
13.3 How do we model evolutionary rates?
13.4 Environments and evolutionary rates
13.4.1 Evolutionary rates of pathogens
13.5 Large-scale genomic changes: duplications/loss and horizontal gene acquisition
13.5.1 Rates of gene duplication and loss
13.5.2 Highways of horizontal gene transfers
13.6 Conclusions
References
Index
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