Environmental Microbiology E-Book

Eugene L. Madsen

• Herausgeber: John Wiley & Sons
• Kategorie: Wissenschaft und neue Technologien
• Sprache: Englisch

Seitenzahl: 1125

Veröffentlichungsjahr: 2015

Beschreibung

New and expanded for its second edition, Environmental Microbiology: From Genomes to Biogeochemistry¸ Second Edition, is a timely update to a classic text filled with ideas, connections, and concepts that advance an in-depth understanding of this growing segment of microbiology. Core principles are highlighted with an emphasis on the logic of the science and new methods-driven discoveries. Numerous up-to-date examples and applications boxes provide tangible reinforcement of material covered. Study questions at the end of each chapter require students to utilize analytical and quantitative approaches, to define and defend arguments, and to apply microbiological paradigms to their personal interests. Essay assignments and related readings stimulate student inquiry and serve as focal points for teachers to launch classroom discussions. A companion website with downloadable artwork and answers to study questions is also available.

Environmental Microbiology: From Genomes to Biogeochemistry, Second Edition, offers a coherent and comprehensive treatment of this dynamic, emerging field, building bridges between basic biology, evolution, genomics, ecology, biotechnology, climate change, and the environmental sciences.

Leseprobe

Environmental Microbiology

From Genomes to Biogeochemistry

SECOND EDITION

Eugene L. Madsen

Department of Microbiology

Cornell University

Ithaca, New York

Copyright © 2016 by Eugene L. Madsen. All rights reserved

Published by John Wiley & Sons, Inc., Hoboken, New Jersey Published simultaneously in Canada

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Library of Congress Cataloging-in-Publication Data:Madsen, Eugene L., author. Environmental microbiology : from genomes to biogeochemistry / Eugene L. Madsen. — Second edition. p. ; cm. Includes bibliographical references and index. ISBN 978-1-118-43963-0 (cloth) I. Title. [DNLM: 1. Environmental Microbiology. 2. Biochemical Phenomena. 3. Genome. QW 55] QR100 579'.17—dc23 2015006393

Contents

Preface

About the Companion Website

Chapter 1: Significance, History, and Challenges of Environmental Microbiology

1.1 Core concepts can unify environmental microbiology

1.2 Synopsis of the significance of environmental microbiology

1.3 A brief history of environmental microbiology

1.4 Complexity of our world

1.5 Many disciplines and their integration

Study questions

References

Chapter 2: Formation of the Biosphere: Key Biogeochemical and Evolutionary Events

2.1 Issues and methods in Earth’s history and evolution

2.2 Formation of early planet Earth

2.3 Did life reach Earth from Mars?

2.4 Plausible stages in the development of early life

2.5 Mineral surfaces in marine hydrothermal vents: the early iron/sulfur world could have driven biosynthesis

2.6 Encapsulation (a key to cellular life) and an alternative (nonmarine) hypothesis for the habitat of precellular life

2.7 A plausible definition of the tree of life’s “Last universal common ancestor” (LUCA)

2.8 The rise of oxygen

2.9 Evidence for oxygen and cellular life in the sedimentary record

2.10 The evolution of oxygenic photosynthesis

2.11 Consequences of oxygenic photosynthesis: molecular oxygen in the atmosphere and large pools of organic carbon

2.12 Eukaryotic evolution: endosymbiotic theory and the blending of traits from Archaea and Bacteria

Study questions

References

Further reading

Chapter 3: Physiological Ecology: Resource Exploitation by Microorganisms

3.1 The cause of physiological diversity: diverse habitats provide selective pressures over evolutionary time

3.2 Biological and evolutionary insights from genomics

3.3 Fundamentals of nutrition: carbon- and energy-source utilization provide a foundation for physiological ecology

3.4 Selective pressures: ecosystem nutrient fluxes regulate the physiological status and composition of microbial communities

3.5 Cellular responses to starvation: resting stages, environmental sensing circuits, gene regulation, dormancy, and slow growth

3.6 A planet of complex mixtures in chemical disequilibrium

3.7 A thermodynamic hierarchy describing biosphere selective pressures, energy sources, and biogeochemical reactions

3.8 Using the thermodynamic hierarchy of half reactions to predict biogeochemical reactions in time and space

3.9 Overview of metabolism and the “logic of electron transport”

3.10 The flow of carbon and electrons in anaerobic food chains: syntrophy is the rule

3.11 The diversity of lithotrophic reactions

Study questions

References

Further reading

Chapter 4: A Survey of the Earth’s Microbial Habitats

4.1 Terrestrial biomes

4.2 Soils: geographic features relevant to both vegetation and microorganisms

4.3 Aquatic habitats

4.4 Subsurface habitats: oceanic and terrestrial

4.5 Defining the prokaryotic biosphere: where do prokaryotes occur on Earth?

4.6 Life at the micron scale: an excursion into the microhabitat of soil microorganisms

4.7 Extreme habitats for life and microbiological adaptations

Study questions

References

Chapter 5: Microbial Diversity: Who is Here and How do we Know?

5.1 Defining cultured and uncultured microorganisms

5.2 Approaching a census: an introduction to the environmental microbiological “toolbox”

5.3 Criteria for census taking: recognition of distinctive microorganisms (species)

5.4 Proceeding toward census taking and measures of microbial diversity

5.5 The tree of life: our view of evolution’s blueprint for biological diversity

5.6 A Sampling of key traits of cultured microorganisms from the domains Eukarya, Bacteria, and Archaea

5.7 Placing the “uncultured majority” on the tree of life: what have nonculture-based investigations revealed?

5.8 Viruses: an overview of biology, ecology, and diversity

5.9 Microbial diversity illustrated by genomics, horizontal gene transfer, and cell size

5.10 Biogeography of microorganisms

Study questions

References

Further reading

Chapter 6: Generating and Interpreting Information in Environmental Microbiology: Methods and Their Limitations

1

6.1 How do we know?

6.2 Perspectives from a century of scholars and enrichment-cultivation procedures

6.3 Constraints on knowledge imposed by ecosystem complexity

6.4 Environmental microbiology’s “Heisenberg uncertainty principle”: model systems and their risks

6.5 Fieldwork: being sure sampling procedures are compatible with analyses and goals

6.6 Blending and balancing disciplines from field geochemistry to pure cultures

6.7 Overview of methods for determining the position and composition of microbial communities

6.8 Methods for determining in situ biogeochemical activities and when they occur

6.9 Cloning-based Metagenomics and related methods: procedures and insights

6.10 Cloning-free, next-generation sequencing and omics methods: procedures and insights

6.11 Discovering the organisms responsible for particular ecological processes: linking identity with activity

Study questions

References

Further reading

Note

Chapter 7: Microbial Biogeochemistry: A Grand Synthesis

7.1 Mineral connections: the roles of inorganic elements in life processes

7.2 Greenhouse gases and lessons from biogeochemical modeling

7.3 The “stuff of life”: identifying the pools of biosphere materials whose microbiological transformations drive the biogeochemical cycles

7.4 Elemental biogeochemical cycles: concepts and physiological processes

7.5 Cellular mechanisms of microbial biogeochemical pathways

7.6 Mass balance approaches to elemental cycles

Study questions

References

Further reading

Chapter 8: Special and Applied Topics in Environmental Microbiology

8.1 Other organisms as microbial habitats: ecological relationships

8.2 Microbial residents of plants and humans

8.3 Biodegradation and bioremediation

8.4 BioFilms

8.5 Evolution of catabolic pathways for organic contaminants

8.6 Environmental biotechnology: overview and nine case studies

8.7 Antibiotic resistance

Study questions

References

Chapter 9: Future Frontiers in Environmental Microbiology

9.1 The influence of systems biology on environmental microbiology

9.2 Ecological niches and their genetic basis

9.3 Concepts help define future progress in environmental microbiology

Study questions

References

Glossary

Index

EULA

List of Tables

Chapter 1

Table 1.1

Table 1.2

Table 1.3

Table 1.4

Table 1.5

Chapter 2

Table 2.1

Table 2.2

Table 2.3

Chapter 3

Table 3.1

Table 3.2

Table 3.3

Table 3.4

Table 3.5

Table 3.6

Table 3.7

Table 3.8

Chapter 4

Table 4.1

Table 4.2

Table 4.3

Table 4.4

Table 4.5

Table 4.6

Table 4.7

Table 4.8

Table 4.9

Table 4.10

Table 4.11

Table 4.12

Chapter 5

Table 5.1

Table 5.2

Table 5.3

Table 5.4

Table 5.5

Chapter 6

Table 6.1

Table 6.2

Table 6.3

Table 6.4

Table 1

Table 6.5

Table 6.6

Table 6.7

Table 6.8

Table 1

Table 6.9

Table 6.10

Table 6.11

Table 6.12

Table 6.13

Table 6.14

Chapter 7

Table 7.1

Table 7.2

Table 7.3

Table 7.4

Figure 7.13

Table 7.6

Chapter 8

Table 8.1

Table 8.2

Table 8.3

Table 8.4

Table 8.5

Table 8.6

Table 8.7

Table 8.8

Table 8.9

Table 8.10

Table 8.11

Table 8.12

Table 8.13

Table 8.14

List of Illustrations

Chapter 1

Figure 1.1  Martinus Beijerinck (1851–1931). Founder of the Delft School of Microbiology, M. Beijerinck worked until the age of 70 at the University of Delft, the Netherlands. He made major discoveries in elective enrichment techniques and used them to advance the understanding of how microorganisms transform nitrogen, sulfur, and other elements. (Reproduced with permission from the American Society for Microbiology Archives, USA.)

Figure 1.2 Sergei Winogradsky (1856–1953). A major contributor to knowledge of soil microbiology, S. Winogradsky described microbial cycling of sulfur and nitrogen compounds. He developed the “Winogradsky column” for growing diverse physiological types of aerobic and anaerobic, heterotrophic and photosynthetic bacteria across gradients of oxygen, sulfur, and light. (Reproduced with permission from the Smith College Archives, Smith College, USA.)