ebook ebooks e-book e-books downloaden bei MyEbooks.ch downloaden

Geomicrobiology: Molecular and Environmental Perspective

:	Larry L. Barton, Martin Mandl, Alexander Loy
:	Alexander Loy, Martin Mandl, Larry Barton
:	Geomicrobiology: Molecular and Environmental Perspective
:	Springer-Verlag
:	9789048192045
:	1
:	CHF 193.20
:

:	Mikrobiologie
:	English

:	437
:	Wasserzeichen/DRM
:	PC/MAC/eReader/Tablet
:	PDF

The interaction of microorganisms with geological activities results in processes influencing development of the Earth's geo- and biospheres. In assessing these microbial functions, scientists have explored short- and longterm geological changes attributed to microorganisms and developed new approaches to evaluate the physiology of microbes including microbial interaction with the geological environment. As the field of geomicrobiology developed, it has become highly interdisciplinary and this book provides a review of the recent developments in a cross section of topics including origin of life, microbial-mineral interactions and microbial processes functioning in marine as well as terrestrial environments. A major component of this book addresses molecular techniques to evaluate microbial evolution and assess relationships of microbes in complex, natural c- munities. Recent developments in so-called 'omics' technologies, including (meta) genomics and (meta)proteomics, and isotope labeling methods allow new insights into the function of microbial community members and their possible geological impact. While this book summarizes current knowledge in various areas, it also reveals unresolved questions that require future investigations. Information in these chapters enhances our fundamental knowledge of geomicrobiology that contributes to the exploitation of microbial functions in mineral and environmental biotechn- ogy applications. It is our hope that this book will stimulate interest in the general field of geomicrobiology and encourage others to explore microbial processes as applied to the Earth.

	Preface	6
	Contents	8
	List of Authors	10
	Chapter 1: Chemoautotrophic Origin of Life: The Iron–Sulfur World Hypothesis	16
	Introduction	16
	Retrodicting the Origin from the Chemical Elements of Life	18
	On the Minimal Organization of the Pioneer Organism	21
	Metabolic Reproduction and Evolution of the Pioneer Organism	23
	Volcanic Flow Setting of the Pioneer Organism	26
	Experimental Synthetic Reactions	30
	Activated Acetic Acid Thioester	30
	Pathways to a-Hydroxy Acids and a-Amino Acids	31
	Activation of a-Amino Acids and Peptide Cycle	31
	Emergence of the Genetic Machinery and Enzymatization of the Metabolism	32
	Cellularization	34
	Inorganic Cells?	34
	Lipid Synthesis	35
	Surface Lipophilization	36
	Semi-cellular Structures	38
	Origin of Chemiosmosis	38
	Pre-cells and the Dawn of Speciation	39
	Divergence of the Domains Bacteria and Archaea	42
	Divergence of the Domain Eukarya	45
	Natural-Historic Considerations	46
	References	47
	Chapter 2: Evolution of Metabolic Pathways and Evolution of Genomes	51
	The Microbial Role in Geochemistry	51
	Origin and Evolution of Metabolic Pathways	55
	From Ancestral to Extant Genomes	55
	The Primordial Metabolism	56
	The Role of Duplication and Fusion of DNA Sequences in the Evolution of Metabolic Pathways in the Early Cells	57
	The Starter Types	57
	The Explosive Expansion of Metabolism in the Early Cells	57
	Gene Duplication	57
	Fate of Duplicated Genes	58
	Gene Fusion	59
	Hypotheses on the Origin and Evolution of Metabolic Pathways	60
	The Retrograde Hypothesis	60
	The Patchwork Hypothesis	61
	The Role of Horizontal Gene Transfer in the Evolution of Genomes and Spreading of Metabolic Functions	62
	The Nitrogen Cycle	63
	Nitrification	64
	Denitrification	65
	Anaerobic Ammonia Oxidation (ANAMMOX)	65
	Ammonification	65
	Nitrogen Fixation: A Paradigm for the Evolution of Metabolic Pathways	65
	Is Nitrogen Fixation an Ancestral Character?	67
	How Many Genes were Involved in the Ancestral Nitrogen Fixation?	68
	How Did the nif Genes Originate and Evolve?	68
	Which were the Molecular Mechanisms Involved in the Spreading of Nitrogen Fixation?	75
	Conclusions	77
	References	79
	Chapter 3: Novel Cultivation Strategies for Environmentally Important Microorganisms	83
	The Significance of Culture-Based Approaches	83
	Basic Requirements of the Bacterial Cell	84
	Principles of the Selective Enrichment	86
	Improved Classical and Advanced Cultivation Methods	88
	Determining Potential Growth Substrates	88
	Mimicking the Chemical Composition in the Natural Environment	90
	Effect of Cyclic Adenosine Monophosphate (cAMP)	92
	Mimicking the Physical Structure and Heterogeneity of the Natural Environment: Polymer Matrices, Solid Surfaces and Defined Laboratory Gradient Systems	93
	Removal of Inhibitors and Avoiding the Formation of Toxic Compounds and Oxygen Radicals	94
	Removal or Selective Inhibition of Bacterial Competitors	96
	Exploiting Positive Interactions Between Bacteria: Cocultivation and Dialysis Cultures	97
	Techniques for the Isolation of Individual Cells	98
	References	101
	Chapter 4: Environmental Proteomics: Studying Structure and Function of Microbial Communities	104
	Introduction	104
	Open Questions in Microbial Ecology	104
	Historical Retrospective of “Omics” Technologies	105
	Environmental Proteomics – A Babylonian Confusion?	107
	Potential Applications of Environmental Proteomics	107
	State-of-the-Art Proteomics Technologies	108
	Sample Preparation	108
	Protein/Peptide Separation and Mass Spectrometry Analyses	110
	Data Analysis and Protein Identification	111
	Data Evaluation	112
	Current Environmental Proteomics Studies – Where Are We So Far?	112
	Community Proteomics of Marine Symbionts of Riftia pachyptila	112
	Whole-Community Proteomics of Richmond Acid Mine Drainage (AMD) Mixed Biofilms	114
	Proteome Analyses of Waste Water Treatment Plants and Activated Sludge	114
	Community Proteomics of Animal and Human Intestinal Tracts	115
	Metaproteome Analyses of Ocean Water	115
	Metaproteome Studies of Highly Complex Groundwater and Soil Environments	116
	Future Perspectives and Final Remarks	116
	Improvements of Mass Spectrometer Sensitivity and Accuracy	117
	Quantitative Metaproteomics – Dream or Reality?	117
	Final Remarks	118
	References	118
	Chapter 5: Analysis of Microbial Communities by Functional Gene Arrays	122
	Introduction	122
	Functional Gene Array Development	123
	Comparison of FGA to Other High-Throughput Genomic Technologies	124
	Design and Development of Geochip	126
	Probe Design	126
	Target Preparation	127
	Hybridization	128
	Image Analysis	128
	Data Analysis	129
	Important Issues for Microarray Application	130
	Application of GeoChip for Microbial Community Analysis	132
	Summary	134
	References	135
	Chapter 6: Probing Identity and Physiology of Uncultured Microorganisms with Isotope Labeling Techniques	140
	Introduction	140
	The Principle of Substrate-Mediated Isotope Labeling Techniques	141
	Community-Wide Screening Approaches	143
	Stable Isotope Probing of Phospholipid-Derived Fatty Acids	143
	Stable Isotope Probing of Nucleic Acids (DNA/RNA-SIP)	146
	Directed Phylogenetic Oligonucleotide Probe-Based Approaches: From Communities to Single Cells	148
	What to Keep in Mind When Using rRNA-Targeted Oligonucleotide Probes/Primers	148