97,99 €
Mehr erfahren.
- Herausgeber: John Wiley & Sons
- Kategorie: Wissenschaft und neue Technologien
- Sprache: Englisch
This well-referenced, inquiry-driven text presents an up-to-date and comprehensive understanding of the emerging field of environmental microbiology. * * Coherent and comprehensive treatment of the dynamic, emerging field of environmental microbiology * Emphasis on real-world habitats and selective pressures experienced by naturally occurring microorganisms * Case studies and "Science and the Citizen" features relate issues in the public's mind to the underlying science * Unique emphasis on current methodologies and strategies for conducting environmental microbiological research, including methods, logic, and data interpretation
Sie lesen das E-Book in den Legimi-Apps auf:
Seitenzahl: 741
Veröffentlichungsjahr: 2011
Ähnliche
CONTENTS
Preface
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
FURTHER READING
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: the early iron/sulfur world could have driven biosynthesis
2.6 Encapsulation: a key to cellular life
2.7 A plausible definition of the tree of life's “last universal common ancestor”
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
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
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 135 microorganisms
4.7 Extreme habitats for life and microbiological adaptations
STUDY QUESTIONS
REFERENCES
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 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
STUDY QUESTIONS
REFERENCES
FURTHER READING
6 Generating and Interpreting Information in Environmental Microbiology: Methods and their Limitations
6.1 How do we know?
6.2 Perspectives from a century of scholars and enrichment-culturing 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 Metagenomics and related methods: procedures and insights
6.10 Discovering the organisms responsible for particular ecological processes: linking identity with activity
STUDY QUESTIONS
REFERENCES
FURTHER READING
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
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 eight case studies
8.7 Antibiotic resistance
STUDY QUESTIONS
REFERENCES
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
Preface
Over the past 20 years, environmental microbiology has emerged from a rather obscure, applied niche within microbiology to become a prominent, ground-breaking area of biology. Environmental microbiology's rise in scholarly stature cannot be simply explained. But one factor was certainly pivotal in bringing environmental microbiology into the ranks of other key biological disciplines. That factor was molecular techniques. Thanks largely to Dr. Norman Pace (in conjunction with his many students) and Gary Olson and Carl Woese, nucleic acid analysis procedures began to flow into environmental microbiology in the mid-1980s. Subsequently, a long series of discoveries have flooded out of environmental microbiology. This two-way flow is constantly accelerating and the discoveries increasingly strengthen the links between environmental microbiology and core areas of biology that include evolution, taxonomy, physiology, genetics, environment, genomics, and ecology.
This textbook has grown from a decade of efforts aimed at presenting environmental microbiology as a coherent discipline to both undergraduate and graduate students at Cornell University. The undergraduate course was initially team-taught by Drs. Martin Alexander and William C. Ghiorse. Later, W. C. Ghiorse and I taught the course. Still later I was the sole instructor. Still later I became instructor of an advanced graduate version of the course. The intended audience for this text is upper-level undergraduates, graduate students, and established scientists seeking to expand their areas of expertise.
Environmental microbiology is inherently multidisciplinary. It provides license to learn many things. Students in university courses will rebel if the subject they are learning fails to develop into a coherent body of knowledge. Thus, presenting environmental microbiology to students in a classroom setting becomes a challenge. How can so many disparate areas of science (e.g., analytical chemistry, geochemistry, soil science, limnology, public health, environmental engineering, ecology, physiology, biogeochemistry, evolution, molecular biology, genomics) be presented as a unified body of information?
This textbook is my attempt to answer that question. Perfection is always evasive. But I have used five core concepts (see Section 1.1) that are reiterated throughout the text, as criteria for selecting and organizing the contents of this book.
The majority of figures presented in this book appear as they were prepared by their original authors in their original sources. This approach is designed to illustrate for the reader that advancements in environmental microbiology are a community effort.
A website with downloadable artwork and answers to study questions is available to instructors at http://www.blackwellpublishing.com/madsen
I hope this book will stimulate new inquiries into what I feel is one of the most fascinating current areas of science. I welcome comments, suggestions, and feedback from readers of this book. I thank the many individuals who provided both direct and indirect sources of information and inspiration. I am particularly grateful to P. D. Butler for assistance in manuscript preparation, to J. Yavitt who guided me to the right destinations in the biogeochemistry literature, and to W. C. Ghiorse for his unbounded enthusiasm for the art and science of microbiology. Constructive comments from several anonymous reviewers are acknowledged. I also apologize for inadvertently failing to include and/or acknowledge scientific contributions from fellow environmental micro- biologist friends and colleagues.
Eugene Madsen
1
Significance, History, and Challenges of Environmental Microbiology
This chapter is designed to instill in the reader a sense of the goals, scope, and excitement that permeate the discipline of environmental microbiology. We begin with five core concepts that unify the field. These are strengthened and expanded throughout the book. Next, an overview of the significance of environmental microbiology is presented, followed by a synopsis of key scholarly events contributing to environmental microbiology's rich heritage. The chapter closes by reminding the reader of the complexity of Earth's biogeochemical systems and that strategies integrating information from many scientific disciplines can improve our understanding of biosphere function.
Chapter 1 Outline
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
1.1 CORE CONCEPTS CAN UNIFY ENVIRONMENTAL MICROBIOLOGY
Environmental microbiology is inherently multidisciplinary. Its many disparate areas of science need to be presented coherently. To work toward that synthesis, this text uses five recurrent core concepts to bind and organize facts and ideas.
Core concept 1. Environmental microbiology is like a child's picture of a house - it has (at least) five sides (a floor, two vertical sides, and two sloping roof pieces). The floor is evolution. The walls are thermodynamics and habitat diversity. The roof pieces are ecology and physiology. To learn environmental microbiology we must master and unite all sides of the house.
Core concept 2. The prime directive for microbial life is survival, maintenance, generation of adenosine triphosphate (ATP), and sporadic growth (generation of new cells). To predict and understand microbial processes in real-world waters, soils, sediments, and other habitats, it is helpful to keep the prime directive in mind.
Core concept 3. There is a mechanistic series of linkages between our planet's habitat diversity and what is recorded in the genomes of microorganisms found in the world today. Diversity in habitats is synonymous with diversity in selective pressures and resources. When operated upon by forces of evolution, the result is molecular, metabolic, and physiological diversity found in extant microorganisms and recorded in their genomes.
Core concept 4. Advancements in environmental microbiology depend upon convergent lines of independent evidence using many measurement procedures. These include microscopy, biomarkers, model cultivated microorganisms, molecular biology, and genomic techniques applied to laboratory and field-based investigations.
Core concept 5. Environmental microbiology is a dynamic, methods limited discipline. Each methodology used by environmental microbiologists has its own set of strengths, weaknesses, and potential artifacts. As new methodologies deliver new types of information to environmental microbiology, practitioners need a sound foundation that affords interpretation of the meaning and place of the incoming discoveries.
1.2 SYNOPSIS OF THE SIGNIFICANCE OF ENVIRONMENTAL MICROBIOLOGY
With the formation of planet Earth 4.6 × 109 years ago, an uncharted series of physical, chemical, biochemical, and (later) biological events began to unfold. Many of these events were slow or random or improbable. Regardless of the precise details of how life developed on Earth, (see Sections 2.3–2.7), it is now clear that for ~70% of life's history, prokaryotes were the sole or dominant life forms. Prokaryotes (Bacteria and Archaea) were (and remain) not just witnesses of geologic, atmospheric, geochemical, and climatic changes that have occurred over the eons. Prokaryotes are also active participants and causative agents of many geochemical reactions found in the geologic record. Admittedly, modern eukaryotes (especially land plants) have been major biogeochemical and ecological players on planet Earth during the most recent 1.4 × 109 years. Nonetheless, today, as always, prokaryotes remain the “hosts” of the planet. Prokaryotes comprise ~60% of the total biomass (Whitman et al., 1998; see Chapter 4), account for as much as 60% of total respiration of some terrestrial habitats (Velvis, 1997; Hanson et al., 2000), and also colonize a variety of Earth's habitats devoid of eukaryotic life due to topographic, climatic and geochemical extremes of elevation, depth, pressure, pH, salinity, heat, or light.
The Earth's habitats present complex gradients of environmental conditions that include variations in temperature, light, pH, pressure, salinity, and both inorganic and organic compounds. The inorganic materials range from elemental sulfur to ammonia, hydrogen gas, and methane and the organic materials range from cellulose to lignin, fats, proteins, lipids, nucleic acid, and humic substances (see Chapter 7). Each geochemical setting (e.g., anaerobic peatlands, oceanic hydrothermal vents, soil humus, deep subsurface sediments) features its own set of resources that can be physiologically exploited by microorganisms. The thermodynamically governed interactions between these resources, their settings, microorganisms themselves, and 3.6 × 109 years of evolution are probably the source of metabolic diversity of the microbial world.
Table 1.1 Microorganisms' unique combination of traits and their broad impact on the biosphere
Microorganisms are the primary agents of geochemical change. Their unique combination of traits (Table 1.1) cast microorganisms in the role of recycling agents for the biosphere. Enzymes accelerate reaction rates between thermodynamically unstable substances. Perhaps the most ecologically important types of enzymatic reactions are those that catalyze oxidation/reduction reactions between electron donors and electron acceptors. These allow microorganisms to generate metabolic energy, survive, and grow. Microorganisms procreate by carrying out complex, genetically regulated sequences of biosynthetic and assimilative intracellular processes. Each daughter cell has essentially the same macro-molecular and elemental composition as its parent. Thus, integrated metabolism of all nutrients (e.g., carbon, nitrogen, phosphorus, sulfur, oxygen, hydrogen, etc.) is implicit in microbial growth. This growth and survival of microorganisms drives the geochemical cycling of the elements, detoxifies many contaminant organic and inorganic compounds, makes essential nutrients present in the biomass of one generation available to the next, and maintains the conditions required by other inhabitants of the biosphere (Table 1.1). Processes carried out by microorganisms in soils, sediments, oceans, lakes, and groundwaters have a major impact on environmental quality, agriculture, and global climate change. These processes are also the basis for current and emerging biotechnologies with industrial and environmental applications (see Chapter 8). Table 1.2 presents a sampling of the ecological and biogeochemical processes that microorganisms catalyze in aquatic or terrestrial habitats. Additional details of biogeochemical processes and ways to recognize and understand them are presented in Chapters 3 and 7.
Table 1.2 Examples of nutrient cycling and physiological processes catalyzed by microorganisms in biosphere habitats (reproduced with permission from Nature Reviews Microbiology from Madsen, E.L. 2005. Identifying microorganisms responsible for ecologically significant biogeochemical processes. Nature Rev. Microbiol. 3:439–446. Macmillan Magazines, http://www.nature.com/reviews)
Fw, freshwater; FwS, freshwater sediment; Gw, groundwater; Os, ocean sediments; Ow, ocean waters; Si, soil; Sw, sewage.
1.3 A BRIEF HISTORY OF ENVIRONMENTAL MICROBIOLOGY
Early foundations of microbiology rest with microscopic observations of fungal sporulation (by Robert Hooke in 1665) and “wee animalcules” - true bacterial structures (by Antonie van Leeuwenhoek in 1684). In the latter half of the nineteenth century, Ferdinand Cohn, Louis Pasteur, and Robert Koch were responsible for methodological innovations in aseptic technique and isolation of microorganisms (Madigan and Martinko, 2006). These, in turn, allowed major advances pertinent to spontaneous generation, disease causation, and germ theory.
Environmental microbiology also experienced major advancements in the nineteenth century; these extend through to the present. Environmental microbiology's roots span many continents and countries (Russia, Japan, Europe, and England) and a complex tapestry of contributions has developed. To a large degree, the challenges and discoveries in environmental microbiology have been habitat-specific. Thus, one approach for grasping the history and traditions of environmental microbiology is to recognize subdisciplines such as marine microbiology, soil microbiology, rumen microbiology, sediment microbiology, geomicrobiology, and subsurface microbiology. In addition, the contributions from various centers of training can also sometimes be easily discerned. These necessarily revolved around various investigators and the institutions where they were based.
As early as 1838 in Germany, C. G. Ehrenberg was developing theories about the influence of the bacterium, Gallionella ferruginea, on the generation of iron deposits in bogs (Ehrlich, 2002). Furthermore, early forays into marine microbiology by A. Certes (in 1882), H. L. Russell, P. Regnard, B. Fischer, and P. and G. C. Frankland allowed the completion of preliminary surveys of microorganisms from farranging oceanic waters and sediments (Litchfield, 1976).
At the University of Delft (the Netherlands) near the end of the nineteenth century, M. W. Beijerinck (Figure 1.1) founded the Delft School traditions of elective enrichment techniques (see Section 6.2) that allowed Beijerinck's crucial discoveries including microbiological transformations of nitrogen and carbon, and also other elements such as manganese (van Niel, 1967; Atlas and Bartha, 1998; Madigan and Martinko, 2006). The helm of the Delft School changed hands from Beijerinck to A. J. Kluyver, and the traditions have been continued in the Netherlands, Germany, and other parts of Europe through to the present. After training in Delft with Beijerinck and Kluyver, C. B. van Niel was asked by L. G. M. Baas Becking to established a research program at Stanford University's Hopkins Marine Station (done in 1929), where R. Y. Stainer, R. Hungate, M. Doudoroff and many others were trained, later establishing their own research programs at other institutions in the United States (van Niel, 1967).
S. Winogradsky (Figure 1.2) is regarded by many as the founder of soil microbiology (Atlas and Bartha, 1998). Working in the latter part of the nineteenth and early decades of the twentieth centuries, Winogradsky's career contributed immensely to our knowledge of soil and environmental microbiology, especially regarding microbial metabolism of sulfur, iron, nitrogen, and manganese. In 1949, much of Winogradsky's work was published as a major treatise entitled, Microbiologie du sol, problemes et methods: cinquante ans de recherches. Oeuvres Completes(Winogradsky, 1949).
Many of the marine microbiologists in the early twentieth century focused their attention on photoluminescent bacteria (E. Pluger, E. W. Harvey, H. Molisch, W. Beneche, G. H. Drew, and J. W. Hastings). Later, transformation by marine microorganisms of carbon and nitrogen were explored, as well as adaptation to low-temperature habitats (S. A. Waksman, C. E. ZoBell, S. J. Niskin, O. Holm-Hansen, and N. V. and V. S. Butkevich). The mid-twentieth century marine studies continued exploration of the physiological and structural responses of microorganisms to salt, low temperature, and pressure (J. M. Shewan, H. W. Jannasch, R. Y. Morita, R. R. Colwell, E. Wada, A. Hattori, and N. Taga). Also, studies of nutrient uptake (J. E. Hobbie) and food chains constituting the “microbial loop” were conducted (L. R. Pomeroy).
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 theunderstanding 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. Winogradsy 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.)
At Rutgers University, Selman A. Waksman was perhaps the foremost American scholar in the discipline of soil microbiology. Many of the Rutgers traditions in soil microbiology were initiated by J. Lipman, Waksman's predecessor (R. Bartha, personal communication; Waksman, 1952). Waksman produced numerous treatises that summarized the history, status, and frontiers of soil microbiology, often in collaboration with R. Starkey. Among the prominent works published by Waksman are “Soil microbiology in 1924: an attempt at an analysis and a synthesis” (Waksman, 1925), Principles of Soil Microbiology (Waksman, 1927), “Soil microbiology as a field of science” (Waksman, 1945), and Soil Microbiology (Waksman, 1952). A steady flow of Rutgers-based contributions to environmental microbiology continue to be published (e.g., Young and Cerniglia, 1995; Haggblom and Bossert, 2003).
In the 1920s and 1930s, E. B. Fred and collaborators, I. L. Baldwin and E. McCoy, comprised a unique cluster of investigators whose interests focused on the Rhizobiumlegume symbiosis. Several decades later at the University of Wisconsin, T. D. Brock and his students made important contributions to microbial ecology, thermophily, and general microbiology. Another graduate of the University of Wisconsin, H. L. Ehrlich earned a Ph.D. in 1951 and, after moving to Rensselaer Polytechnic Institute, carried out studies on the bacteriology of manganese nodules, among other topics. Author of four comprehensive editions of Geomicrobiology, H. L. Ehrlich is, for many, the founder of this discipline.
Another University of Wisconsin graduate, M. Alexander, moved to Cornell University in 1955. For four decades prior to Alexander's arrival, soil microbiological research was conducted at Cornell by J. K. Wilson and F. Broadbent. From 1955 to the present, Alexander's contributionsto soil microbiology have examined a broad diversity of phenomena, which include various transformations of nitrogen, predatorprey relations, microbial metabolism of pesticides and environmental pollutants, and advancements in environmental toxicology. Many environmental micro-biologists have received training with M. Alexander and become prominent investigators, including J. M. Tiedje.
Other schools and individuals in Britain, Italy, France, Belgium and other parts of Europe, Japan, Russia and other parts of Asia, Africa, Australia, the United States and other parts of the Americas certainly have contributed in significant ways to advancements in environmental microbiology. An insightful review of the history of soil microbiology, with special emphasis on eastern European and Russian developments was written by Macura (1974).
The many historical milestones in the development of environmental microbiology (most of which are shared with broader fields of biology and microbiology) have been reviewed by Atlas and Bartha (1998), Brock (1961), Lechevalier and Solotorovsky (1965), Macura (1974), Madigan and Martinko (2006), van Niel (1967), Waksman (1925, 1927, 1952), and others. Some of the highlights are listed in Table 1.3.
Table 1.3 Selected landmark events in the history of environmental microbiology
Figure 1.3 Watershed in a temperate forest ecosystem. Arrows show the inputs and outflows from the system. Reservoirs for carbon, nitrogen, and other nutrients includebiomass, soil litter layer, soil mineral layer, subsoil, snow, streams, and lakes. Dominant physiological processes carried out by biota include photosynthesis, grazing, decomposition, respiration, nitrogen fixation, ammonification, and nitrification. Key abiotic processes include insolation (sunlight), transport, precipitation, runoff, infiltration, dissolution, and acid/base and oxidation/reduction reactions (see Table 1.4). Net budgets can be constructed for ecosystems; when inputs match outputs, the systems are said to be “steady state”.
As this historical treatment reaches into the twenty-first century, the branches and traditions in environmental microbiology become so complex that patterns of individual contributions become difficult to discern. A complete list of schools, individual investigators, and their respective discoveries is beyond the scope of this section. The author apologizes for his biases, limited education, and any and all inadvertent omissions that readers may notice in this brief historical overview.
1.4 COMPLEXITY OF OUR WORLD
Although we humans are capable of developing ideas or concepts or models that partially describe the biosphere we live in, real-world complexity of ecological systems and subsystems remains generally beyond full scientific description. Figure 1.3 and 1.4 are designed to begin to develop for the reader a sense of the complexity of real-world ecosystems - in this case a temperate forested watershed. The watershed depicted in Figure 1.3 is open (energy and materials flow through it) and features dynamic changes in time and space. The watershed system contains many components ranging from the site geology and soils to both small and large creatures, including microorganisms. Climate-related influences are major variables that, in turn, cause variations in how the creatures and their habitat interact. Biogeochemical processes are manifestations of such interactions. These processes include chemical and physical reactions, as well as the diverse physiological reactions and behavior (Table 1.4). The physical, chemical, nutritional, and ecological conditions for watershed inhabitants vary from the scale of micrometers to kilometers. Regarding temporal variability, in situ processes that directly and indirectly influence fluxes of materials into, out of, and within the system are also dynamic.
Table 1.4 Types of biogeochemical processes that typically occur and interact in real-world habitats
At the scale of ~1 m, humans are able to survey habitats and map the occurrence of both abiotic (rocks, soils, gasses, water) and biotic (plants, animals) components of the watershed. At this scale, much progress has been made toward understanding ecosystems. Biogeochemical ecosystem ecologists have gained far-reaching insights into how such systems work by performing a variety of measurements in basins whose sealed bedrock foundations allow ecosystem budgets to be constructed (Figure 1.3). When integrated over time and space, the chemical constituents (water, carbon, nitrogen, sulfur, etc.) measured in incoming precipitation, in outflowing waters, and in storage reservoirs (lakes, soil, the biota) can provide a rigorous basis for understanding how watersheds work and how they respond to perturbations (Likens and Bormann, 1995). Understanding watershed (as well as global) biogeochemical cycles relies upon rigorous data sets and well-defined physical and conceptual boundaries. For a given system, regardless of its size, if it is in steady state, the inputs must equal the outputs (Figure 1.3). By the same token, if input and output terms for a given system are not in balance, key biogeochemical parameters of interest may be changing with time. Net loss or gain is dependent on relative rates of consumption and production. Biogeochemical data sets provide a means for answering crucial ecological questions such as: Is the system in steady state? Are carbon and nitrogen accruing or diminishing? Does input of atmospheric pollutants impact ecosystem function? What goods and services do intact watersheds provide in terms of water and soil quality? More details on measuring and modeling bio-geochemical cycles are presented in Chapter 7.
Large-scale watershed data capture net changes in complex, open systems. Though profound and insightful, this approach leaves mechanistic microscale cause-and-effect linkages unaddressed. Measures of net change do not address dynamic controls on rates of processes that generate (versus those that consume) components of a given nutrient pool. Indeed, the intricate microscale interactions between biotic and abiotic field processes are often masked in data gathered in large-scale systems. Thus, ecosystem-level biogeochemical data may often fail to satisfy the scientific need for details of the processes of interest. An example of steps toward a mechanistic understanding of ecosystem process is shown in Figure 1.4. This model shows a partial synthesis of ecosystem processes that govern the fate of nitrogen in a watershed. Inputs, flows, nutrient pools, biological players, physiological reactions, and transport processes are depicted. Understanding and measuring the sizes of nitrogenous pools, their transformations, rates, fluxes, and the active biotic agents represents a major challenge for both biogeochemists and microbiologists. Yet Figure 1.4 considerably simplifies the processes that actually occur in real-world watersheds because many details are missing and comparably complex reactions and interactions apply simultaneously to other nutrient elements (C, S, P, O, H, etc.). Consider a data set in which concentrations of ammonium (a key form of nitrogen) are found to fluctuate in stream sediments. Interpreting such field measurements is very difficult because the ammonium pool at any given moment is controlled by processes of production (e.g., ammonification by microorganisms), consumption (e.g., aerobic and anaerobic ammonia-oxidizing microorganisms, nutrient uptake by all organisms) and transport (e.g., entrainment in flowing water, diffusion, dilution, physical disturbance of sediment). Clearly, the many compounded intricacies of nutrient cycling and trophic and biochemical interactions in a field habitat make biogeochemical processes, especially those catalyzed by microorganisms, difficult to decipher.
1.5 MANY DISCIPLINES AND THEIR INTEGRATION
Answer: The optimistic answer to these questions is simple: We use the many tools on hand to twenty-first century science.
Figure 1.4 Flow model of nitrogen (N) cycling in terrestrial ecosystems. Shown are basic inputs, storages, microbial processes, outputs, and both biotic and abiotic interactions. (Reprinted and modified with permission from Madsen, E.L. 1998. Epistemology of environmental microbiology. Environ. Sci. Technol. 32:429–439. Copyright 1998, American Chemical Society.)
Table 1.5 Disciplines that contribute to environmental microbiology
The principles are sound, the insights are broad, and the sophisticated technologies are ever expanding. To counterbalance the challenges of ecosystem complexity, we can utilize: (i) robust, predictable rules of chemical thermodynamics, geochemical reactions, physiology, and biochemistry; (ii) measurement techniques from analytical chemistry, hydrogeology, physiology, microbiology, molecular biology; and (iii) compound-specific properties such as solubility, volatility, toxicity, and susceptibility to biotic and abiotic reactions. A partial listing of the many areas of science that contribute to advancements in environmental microbiology, with accompanying synopses and references, appears in Table 1.5.
Conceptually, environmental microbiology resides at the interface between two vigorously expanding disciplines: environmental science and microbial ecology (Figure 1.5). Both disciplines (spheres in Figure 1.5) seek to understand highly complex and underexplored systems. Each discipline currently consists of a significant body of facts and principles (green inner areas of spheres in Figure 1.5), with expanding zones of research (pink bands). But the chances are high that information awaiting discovery (blue areas) greatly exceeds current knowledge. For example, nearly all current information about prokaryotic microorganisms is based upon measurements performed on less than 6500 isolated species. These cultivated species represent approximately 0.1% of the total estimated diversity of microorganism in the biosphere (see Sections 5.1–5.7). The exciting new discoveries in environmental microbiology emerge by examining how microorganisms interact with their habitats (central downward arrow in Figure 1.5).
Figure 1.5 Conceptual representation of how the disciplines of environmental science (left sphere) and microbial ecology (right sphere) interact to allow new discoveries at the interface between microorganisms and their habitats. Information in each discipline is depicted as a combination of current knowledge, current frontiers, and knowledge awaiting discovery. Microbial Ecology and Environmental Microbiology have considerable disciplinary overlap (seeTable 1.5); nonetheless, advancements in the latter are represented by the central, downward arrow. (Reproduced and modified with permission from Nature Reviews Microbiology, from Madsen, E.L. 2005. Identifying microorganisms responsible for ecologically significant biogeochemical processes. Nature Rev. Microbiol. 3:439–446. Macmillan Magazines Ltd, http://www.nature.com/reviews.)
Thus, the path toward progress in environmental microbiology involves multidisciplinary approaches, assembling convergent lines of independent evidence, and testing alternative hypotheses. Ongoing integration of new methodologies (e.g., from environmental science, microbial ecology and other disciplines listed in Table 1.5) into environmental microbiology ensures that the number of lines and the robustness of both their convergence and their tests will increase. A conceptual paradigm that graphically depicts the synergistic relationship between microbiological processes in field sites, reductionistic biological disciplines, and iterative methodological linkages between these disciplines is presented in Figure 1.6.
Figure 1.6 Paradigm for how the integration of disciplines and their respective methodologies can extend knowledge of environmental microbiology. Relationships between microorganisms responsible for field biogeochemical processes, reductionistic disciplines, and their application to microorganisms in field sites are depicted. The three different types of arrows indicate sequential refinements in biological disciplines (large downward-pointing solid arrows), resultant information (small arrows pointing to the right), and innovative methodological applications to naturally occurring microbial communities (dashed arrows). GC/MS, gas chromatography/mass spectrometry; PCR, polymerase chain reaction; RT, reverse transcriptase. (Reprinted and modified with permission from Madsen, E.L. 1998. Epistemology of environmental microbiology. Environ. Sci. Technol. 32:429–439. Copyright 1998, American Chemical Society.)
Observations of microorganisms in natural settings instigate a series of procedures progressing through mixed cultures, pure cultures, and physiological, biochemical, genetic, and molecular biological inquiries that each stand alone scientifically. But appreciable new knowledge of naturally occurring microorganisms is gained when advancements from the pure biological sciences are directed back to microorganisms in their field habitats. These methodological advancements (shown as dashed arrows in Figure 1.6; see Chapter 6 for methodologies and their impacts) and the knowledge they generate accrue with each new cycle from field observations to molecular biology and back. Thus, integration of many disciplines is the path forward in environmental microbiology.
STUDY QUESTIONS
1 Core concept 1 presumes a two-dimensional house like that drawn on paper by school children. If you were to expand the concept to three dimensions, then two more walls would be required to keep the “house of environmental microbiology”from falling down. What two disciplines would you add and why? (Hint: for suggestions see Table 1.5.)
2 Core concept 3 uses the phrase “mechanistic series of linkages between our planet's habitat diversity and what is recorded in the genomes of microorganisms found in the world today”. This is a hypothesis. If you wanted to test the hypothesis by completing measurements and assembling a data set, what would you do? Specifically, what experimental design would readily test the hypothesis? And what would you measure? What methodological barriers might hamper assembling a useful data set? How might these be overcome? (Hint: Sections 3.2 and 3.3 discusses genomic tools. Answer this question before and after reading Chapter 3.)
3 Many names of microorganisms are designed to recognize individual microbiologists who have contributed to the discipline. For instance, the genera Pasteurella, Thauera, and Shewanella are named after people. Similarly, the species designations in Vibrio harveyii,Desulfomonile tiedjei,Thermotoga jannaschii, Nitrobacter winogradkyi, and Acetobacterium woodii are also named for people. Use the world wide web or a resource like Bergey's Manual of Systematic Bacteriology or the International Journal of Systematic and Evolutionary Microbiology to discover the legacy of at least one person memorialized in the name of a microorganism.
4 Go for a walk outside to visit a forest, agricultural field, garden, or pond, stream or other body of water. Sit down and examine (literally, and aided by your imagination) the biotic and abiotic components of a cubic meter of water, sediment, or soil. This cubic meter defines a study system. What to you see? Divide a piece of paper into six columns with the headings “Materials and energy entering and leaving” ,“Inorganic materials”, “Organic materials”, “Organisms”, “Interactions between system components”, and “Biological processes”. Add at least five entries under each column heading. Then imagine how each entry would change over the course of a year. Compare and contrast what you compiled in your listing with information in Figures 1.3–1.6 and Tables 1.2 and 1.4.
REFERENCES
Adrian, L., U. Szewyk, J. Wecke, and H. Görisch. 2000. Bacterial dehalorespiration with chlorinated benzenes. Nature408:580–583.
Albaréde, F. 2003. Geochemistry: An introduction. Cambridge University Press, New York.
Alexander, M. 1999. Biodegradation and Biore-mediation, 2nd edn. Academic Press, San Diego, CA.
Amann, R.I., W. Ludwig, and K.-H. Schleifer. 1995. Phylogenetic identification and in situ detectionof individual microbial cells without cultivation. Microbiol. Rev. 59:143–169.
Amann, R., N. Springer, W. Ludwig, H.-D. Görtz, and K.-H. Schleifer. 1991. Identification in situ and phylogeny of uncultured bacterial endosym-bionts. Nature351:161–164.
Andrews, J.E. 2004. An Introduction to Environmental Chemistry. Blackwell Science, Oxford. Atlas, R.M. and R. Bartha. 1998. Microbial Ecology: Fundamentals and applications, 4th edn. Benjamin Cummings, Menlo Park, CA.
Baxevanis, A.D. and B.F.F. Ouellette. 2001. Bio-informatics: A practical guide to the analysis of genes and proteins, 2nd edn. Wiley Interscience, New York.
Bitton, G.E. 1999. Wastewater Microbiology, 2nd edn Wiley Liss, New York.
Boetius, A., K. Ravenschlag, C.J. Schubert, et al. 2000. A marine microbial consortium apparently mediating anaerobic oxidation of methane. Nature407:623–626.
Boxall, A.B.A., C.J. Sinclair, K. Fenner, D. Kolpin, and S.J. Maund. 2004. When synthetic chemicals degrade in the environment. Environ. Sci. Technol. 38:368A–375A.
Brady, N.C. and R.R. Weil. 1999. The Nature and Properties of Soils, 12th edn. Prentice Hall, Upper Saddle River, NJ.
Brock, T.D. 1961. Milestones in Microbiology. Prentice Hall, Englewood Cliffs, NJ.
Bull, I.D., N.R. Parekh, G.H. Hall, P. Ineson, and R.P. Evershed. 2000. Detection and classification of atmospheric methane oxidizing bacteria in soil. Nature405:175–178.
Burlage, R., R. Atlas, D. Stahl, G. Geesey, and G. Sayler (eds) 1998. Techniques in Microbial Ecology. Oxford University Press, New York.
Chapin, F.S., P.A. Matson, and H.A. Mooney. 2002. Principles of Terrestrial Ecosystem Ecology. Springer Verlag, New York.
Christian, G.D. 2003. Analytical Chemistry, 6th edn.Wiley and Sons, New York.
Coates, J.D. and L.A. Achenbach. 2004. Microbial per-chlorate reduction: rocket-fuelled metabolism. Nature Rev. Microbiol. 2:569–580.
Conrad, R. 1996. Soil microorganisms as controllers of atmospheric trace gases (H2, CO, CH4, OCS, N2O, and NO). Microbiol. Rev. 60:609–640.
Dalsgaard, T., D.E. Canfield, J. Petersen, B. Thamdrup and J. Acuna-González. 2003. N2 production by the anammox reaction in the anoxic water column of Golfo Culce, Costa Rica. Nature422:606–608.
Deeb, R.A., K.-H. Chu, T. Shih, et al. 2003. MTBE and other oxygenates: Environmental sources, analysis, occurrence, and treatment. Environ. Eng. Sci. 20:433–447.
Devlin, T.M. (ed.) 2001. Textbook of Biochemistry with Clinical Correlations, 5th edn. Wiley and Sons, New York.
Edwards, K.J., P.L. Bond, T.M. Gihrling, and J.F. Banfield. 2000. An archaeal iron-oxidizing extreme acidophile important in acid mine drainage. Science287:1796–1799.
Ehrlich, H.L. 2002. Geomicrobiology, 4th edn. Marcel Dekker, New York.
Esteve-Núñez, A., A. Caballero, and J.L. Ramos. 2001. Biological degradation of 2,4,6-trinitro-toluene. Microbiol. Molec. Biol. Rev. 65:335–352.
Fenchel, T., G.M. King, and T.H. Blackburn. 1998. Bacterial Biogeochemistry: The ecophysiology of mineral cycling. Academic Press, San Diego, CA.
Fetter, G.W. 1994. Applied Hydrogeology. Prentice Hall, Upper Saddle River, NJ.
Fifield, F.W. 2000. Principles and Practice of Analytical Chemistry, 5th edn. Blackwell Science, Oxford.
Ford, T.E. (ed.) 1993. Aquatic Microbiology: An ecological approach. Blackwell Scientific Publications, Oxford.
Fred, E.B., I.L. Baldwin, and E. McCoy. 1932. Root Nodule Bacteria and Leguminous Plants. University of Wisconsin Studies of Science No. 5. University of Wisconsin, Madison, WI.
Glick, B.R. and J.J. Pasternack. 2003. Molecular Biotechnology: Principles and application of recombinant DNA, 3rd edn. American Society of Microbiology Press, Washington, DC.
Gottschalk, G. 1986. Bacterial Metabolism, 2nd edn. Springer-Verlag, New York.
Habicht, K.S. and D.E. Canfield. 1996. Sulphur isotope fractionation in modern microbial mats and the evolution of the sulphur cycle. Nature25:342343.
Haggblom, M. and I.D. Bossert (eds) 2003. Dehalogenation: Microbial processes and environmental applications. Kluwer Academic Publications, Boston, MA.
Hanson, P.J., N.T. Edwards, C.T. Garten, and J.A. Andrews. 2000. Separating root and soil microbial contributions to soil respiration: A review of methods and observations. Biogeochemistry48:115–146.
Heemsbergen, D.A. 2004. Biodiversity effects on soil processes explained by interspecific functional dis-similarity. Science306:1019–1020.
Huang, P.M., J.-M. Bollag, and N. Senesi (eds) 2002. Interactions between Soil Particles and Microorganisms: Impact on the terrestrial ecosystem. Wiley and Sons, New York.
Jones, T.H., L.J. Thompson, J.H. Lawton, et al. 1998. Impacts of rising atmospheric carbon dioxide on model terrestrial ecosystems. Science280:441–443.
Karl, D., A. Michaels, B. Bergman, et al. 2002. Dinitrogen fixation in the world's oceans. Bio-geochemistry57/58:47–98.
Kirchman, D.L. (ed.) 2000. Microbial Ecology of the Oceans. Wiley and Sons, New York.
Kowalchuk, G.A. and J.R. Stephen. 2001. Ammonia-oxidizing bacteria: A model for molecular microbial ecology. Annu. Rev. Microbiol. 55:485–529.
Krebs, C.I. 2001. Ecology: The experimental analysis of distribution and abundance. Benjamin Cummings, San Francisco, CA.
Lechevalier, H.A. and M. Solotorovsky. 1965. Three Centuries of Microbiology. McGraw-Hill, New York.
Lengeler, J.W., G. Drews, and H.G. Schlegel (eds) 1999. Biology of Prokaryotes. Blackwell Science, Stuttgart.
Likens, G.E. and F.H. Bormann. 1995. Biogeochemistry of a Forested Ecosystem, 2nd edn. Springer-Verlag, New York.
Litchfield, C.D. (ed.) 1976. Marine Microbiology. Benchmark Papers in Microbiology No. 11. Dowden, Hutchinson and Ross Inc., Stroudsburg, PA.
Lovley, D.R. 2003. Cleaning up with genomics: Applying molecular biology to bioremediation. Nature Rev. Microbiol. 1:35–44.
Macura, J. 1974. Trends and advances in soil microbiology from 1924 to 1974. Geoderma12:311–329.
Madigan, M.T. and J.M. Martinko. 2006. Brock Biology of Microorganisms, 11th edn. Prentice Hall, Englewood Cliffs, NJ.
Madsen, E.L. 1998. Epistemology of environmental microbiology. Environ. Sci. Technol. 32:429–439.
20Madsen, E.L. 2005. Identifying microorganisms responsible for ecologically significant biogeochemical processes. Nature Rev. Microbiol. 3:439–446.
Maier, R.M., I.L. Pepper, and C.P. Gerba. 2000. Environmental Microbiology. Academic Press, San Diego, CA.
Maymo-Gatell, X., Y.T. Chien, J.M. Gossett, and S.H. Zinder. 1997. Isolation of a bacterium that reductively dechlorinates tetrachloroethene to ethene. Science276:1568–1571.
McArthur, J V. 2006. Microbial Ecology: An evolutionary approach. Elsevier Publishing, Amsterdam.
Miller, G.T., Jr. 2004. Living in the Environment: Principles, connections, and solutions, 13th edn. Brooks/ Cole-Thomson Learning Inc., Pacific Grove, CA.
Millero, F.J. 2001. The Physical Chemistry of Natural Waters. Wiley Interscience, New York.
Morel, F.M., A.M.L. Kraepiel, and M. Amyiot. 1998. The chemical cycle and bioaccumulation of mercury. Annu. Rev. Ecol. Systemat. 29:543–566.
Murphy, D.M. 2001. Fundamentals of Light Microscopy and Electronic Imaging. Wiley-Liss, New York.
Nelson, D.L. and M.M. Cox. 2005. Lehninger Principles of Biochemistry, 4th edn. W.H. Freeman, New York.
Nicholls, D.G. and S.J. Ferguson. 2002. Bioenergetics 3. Academic Press, London.
Olsen, G.J., D.J. Lane, S.J. Giovannoni, and N.R. Pace. 1986. Microbial ecology and evolution: A ribosomal RNA approach. Annu. Rev. Microbiol. 40: 337–365.
Oremland, R.S. and F.J. Stolz. 2003. The ecology of arsenic. Science300:939–944.
Osborn, A.M. and C.J. Smith (eds) 2005. Molecular Microbial Ecology. Taylor and Francis, New York.
Pace, N.R. 1997. A molecular view of microbial diversity and the biosphere. Science276:734–740.
Pace, N.R., D.A. Stahl, D.J. Lane, and G.J. Olsen. 1986. The analysis of natural microbial populations by ribosomal RNA sequences. Adv. Microbial Ecol. 9:1–55.
Partensky, F., W.R. Hess, and D. Vaulot. 1999. Prochlorococcus, a marine photosynthetic prokaryote of global significance. Microbiol. Mol. Biol. Rev. 63:106–127.
Pichard, S.L., L. Campbell, K. Carder, et al. 1997. Analysis of ribulose bisphosphate carboxylase gene expression in natural phytoplankton communities by group-specific gene probing. Marine Ecol. Progr. Series149:239–253.
Rickleffs, R.E. and G.L. Miller. 2000. Ecology, 4th edn. W.H. Freeman, New York.
Rittmann, B.E. and P.L. McCarty. 2001. Environmental Biotechnology: Principles and applications. McGraw-Hill, Boston, MA.
Rochelle, P.A. (ed.) 2001. Environmental Molecular Microbiology: Protocols and applications. Horizon Scientific, Wymondham, UK.
Schaechter, M., J.L. Ingraham, and F.C. Niedhardt. 2006. Microbe. American Society for Microbiology Press, Washington, DC.
Schink, B. 1997. Energetics of syntrophic cooperation in methanogenic degradation. Microbiol. Mol. Biol. Rev. 61:262–280.
Schlesinger, W.H. 1997. Biogeochemistry: An analysis of global change, 2nd edn. Academic Press, San Diego, CA.
Schwarzenbach, R.P., P. Gschwend, and D.M. Imboden. 2002. Environmental Organic Chemistry, 2nd edn. Wiley and Sons, New York.
Segers, R. 1998. Methane production and methane consumption: A review of processes underlying wetland methane fluxes. Biogeochemistry41:23–51.
Sensen, C.W. (ed.) 2002. Essentials of Genomics and Bioinformatics. Wiley and Sons, New York.
Sigel, A., H. Sigel, and R. Sigel (eds) 2005. Metal Ions in Biological Systems, Vol. 43. Biogeochemical Cycles of Elements. Marcel Dekker, New York.
Snyder, L. and W. Champness. 2003. Molecular Genetics of Bacteria, 2nd edn. American Society for Microbiology, Washington, DC.
Spain, J.C., J.B. Hughes, and H.-J. Knackmuss (eds) 2000. Biodegradation of Nitroaromatic Compounds and Explosives. Lewis Publishing, Boca Raton, FL.
Spencer, J.F.T. and A.L. Ragout de Spencer (eds) 2004. Environmental Microbiology: Methods and protocols. Humana Press, Totowa, NJ.
Staley, J.T. and A.-L. Reysenbach (eds) 2002. Biodiversity of Microbial Life: Foundation of Earth's biosphere. Wiley and Sons, New York.
Stark, J.M. and S.C. Hart. 1997. High rates of nitrification and nitrate turnover in undisturbed coniferous forests. Nature385:61–64.
Stumm, W. and J.J. Morgan. 1996. Aquatic Chemistry: Chemical equilibria and rates in natural waters, 3rd edn. Wiley and Sons, New York.
Sverdrup, K.A., A.C. Duxbury, and A.B. Duxbury. 2003. An Introduction to the World's Oceans. McGraw-Hill, Boston, MA.
Sylvia, D.M., J.J. Fuhrmann, P.G. Hartel, and D.A. Zuberer. 2005. Principles and Application of SoilMicrobiology, 2nd edn. Prentice Hall, Upper Saddle River, NJ.
Taylor, C.D. and C.O. Wirsen. 1997. Microbiology and ecology of filamentous sulfur formation. Science277:1483–1485.
Tchobanoglous, G., F.L. Burton, and H.D. Stensel. 2002. Wastewater Engineering: Treatment and reuse. McGraw-Hill, New York. Ternes, T.A., A. Joss, and H. Seigrist. 2004.
Scrutinizing personal care products. Environ. Sci. Technol. 38:393A–399A.
Ting, C.S., G. Rocap, J. King, and S.W. Chisholm. 2002. Cyanobacterial photosynthesis in the oceans: the origins and significance of divergent light-harvesting strategies. Trends Microbiol. 10:134–142.
Twyman, R.M. 2004. Principles of Proteomics. BIOS Scientific Publishing, New York.
van Breemen, N., E.W. Boyer, C.L. Goodale, et al. 2002. Where did all the nitrogen go? Fate of nitrogen inputs to large watersheds in the northeastern USA. Biogeochemistry57/58:267–293.
van Elsas, J.D., J.T. Trevors, and E.M.H. Wellington. 1997. Modern Soil Microbiology. Marcel Dekker, New York.
Van Hamme, J.C., A. Singh, and O.P. Ward. 2003. Recent advances in petroleum microbiology. Microbiol. Mol. Biol. Rev. 67:503–549.
van Niel, C.B. 1967. The education of a microbiologist: some reflections. Annu. Rev. Microbiol. 21:130.
van Niftrik, L.A., J.A. Fuerst, J.S.S. Damste, J.G. Kuenen, M.S.M. Jetten, and M. Strous. 2004. The anammoxosome: an intracytoplasmic compartment in anammox bacteria. FEMS Microbiol. Lett. 233:7–31.
Velvis, H. 1997. Evaluation of the selective respiratory inhibition method for measuring the ratio of fungal:bacterial activity in acid agricultural soils. Biol. Fertil. Soils25:354–360.
Waksman, S.A. 1925. Soil microbiology in 1924: an attempt at an analysis and a synthesis. Soil Sci. 19:201–249.
Waksman, S.A. 1927. Principles of Soil Microbiology.Williams and Wilkins, Baltimore, MD.
Waksman, S.A. 1945. Soil microbiology as a field of science. Science102:339–344.
Waksman, S.A. 1952. Soil Microbiology. Wiley and Sons, New York.
Ward, D.M., M.M. Bateson, R. Weller, and A.L. Ruff-Roberts. 1993. Ribosomal RNA analysis of microorganisms as they occur in nature. Adv. Microbial Ecol. 12:219–286.
Wetzel, R.G. 2001. Limnology: Lake and river ecosystems, 3rd edn. Academic Press, San Diego, CA.
Wetzel, R.G. and G.E. Likens. 2000. Limnological Analyses, 3rd edn. Springer-Verlag, New York.
White, D.C. 1994. Is there anything else you need to understand about the microbiota that cannot be derived from analysis of nucleic acids? Microbial Ecol. 28:163–166.
White, D. 1995. The Physiology and Biochemistry of Prokaryotes. Oxford University Press, New York. Whitman, W.B., D.C. Coleman, and W.J. Wiebe. 1998. Prokaryotes: the unseen majority. Proc. Natl. Acad. Sci. USA95:6578–6583.
Winogradsky, S. 1949. Microbiologie du sol, problemes et methods: cinquante ans de recherches. Oeuvres completes. Masson, Paris.
Woese, C.R. 1987. Bacterial evolution. Microbiol. Rev. 51:221–271.
Woese, C.R. 1992. Prokaryotic systematics: the evolution of a science. In: A. Balows, H.G. Truper, M. Dworkin, W. Harder, and K.-H. Schleifer (eds) The Prokaryotes, 2nd edn, pp. 3–18. Springer-Verlag, New York.
Young, L. and C. Cerniglia (eds) 1995. Microbial Transformation and Degradation of Toxic Organic Chemicals. Wiley-Liss, New York.
Zhou, J., D.K. Thompson, Y. Zu, and J.M. Tiedje (eds) 2004. Microbial Functional Genomics. Wiley-Liss, Hoboken, NJ.
Zumft, W.G. 1997. Cell biology and molecular basis of denitrification. Microbiol. Mol. Biol. Rev. 61:533–616.
FURTHER READING
Carter, J.P. and J.M. Lynch. 1993. Immunological and molecular techniques for studying the dynamic of microbial populations and communities in soil. In: J.-M. Bollag and G. Stozky (eds) Soil Biochemistry, Vol. 8, pp. 239–272. Marcel Dekker, New York.
de Duve, C. 2002. Life Evolving: Molecules, mind, and meaning. Oxford University Press, Oxford
2
Formation of the Biosphere: Key Biogeochemical and Evolutionary Events
This chapter provides an overview of the history of Earth and its forms of life. We review state–ofthe–art tools, principles, and logic used to generate information addressing how our world progressed from its ancient prebiotic state to its contemporary biotic state. Key events included: planetary cooling, geochemical reactions at mineral surfaces on the floor of primordial seas, an “RNA world”, development of primitive cells, the “last universal common ancestor”, anoxygenic photosynthesis, oxygenic photosynthesis, the rise of oxygen in the atmosphere, the development of the ozone shield, and the evolution of higher forms of eukaryotes. The chapter closes by reviewing endosymbiotic theory and key biochemical and structural contrasts between prokaryotic and eukaryotic cells.
Chapter 2 Outline
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: the early iron/sulfur world could have driven biosynthesis
2.6 Encapsulation: a key to cellular life
2.7 A plausible definition of the tree of life’s “last universal common ancestor”
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
2.1 ISSUES AND METHODS IN EARTH'S HISTORY AND EVOLUTION
These and related questions have likely been pondered by humans for thousands of years. In our quest for understanding extant microorganisms that dwell in biosphere habitats, it is essential to place them in historical, metabolic, and evolutionary context. To achieve this, we would ideally be able to superimpose continuous, independent timelines derived from the geologic record, the fossil record, the climate record, the evolutionary record, and the molecular phylogenetic record. Conceivably this superimposition could allow cause–and–effect interactions to be documented, linking specific events such as changes in atmospheric composition, glaciation, tectonic movements, and the rise and fall of biotic adaptations. This ideal has not yet been achieved at high resolution. Instead, we have only glimpses here and there of our planet's complex, shrouded past (Table 2.1). However, recent advances have made progress toward achieving a synthesis that may solve the puzzles of Earth's history. The key tools used to discover and decipher planetary history are listed in Table 2.2 and further explained in Boxes 2.1 and 2.2. By knowing Earth's global distribution of land forms, rocks, and minerals, geologists have identified where to look for clues about ancient Earth and life's beginnings (Figure 2.1). Discovery of the clues and their assembly into a convincing, coherent body of knowledge is ongoing – reliant upon insights from geology, paleontology, nuclear chemistry, analytical chemistry, experimental biochemistry, as well as molecular phylogeny (Table 2.2).
2.2 FORMATION OF EARLY PLANET EARTH
Explosions from supernovae 4.6 × 109 years ago are thought to have instigated the formation of our solar system (Nisbet and Sleep, 2001). The inner planets (Earth, Mars, Venus, Mercury) were produced from collisions between planetisemels. Early Earth featured huge pools of surface magma which cooled rapidly (∼2 × 106 years) to ∼100°C. Later, water condensed, creating the oceans. Volcanism and bombardment by meteors were common. These collisions are thought to have repeatedly heated the oceans to >100°C, causing extensive vaporizing of water. Our moon was likely formed 4.5 × 109 years ago when molten mantle was ejected into orbit after Earth was struck by another planet about the size of Mars. Bombardment diminished perhaps by 4.2–4.0 × 109 years ago. The scale of geologic time, from planet formation to the present, is shown in Figure 2.2.
Table 2.1 Key event and conditions of early Earth
Time (109 years before present) Events Conditions4.6Colliding planetisemalsEarth formedMoon formedLoss of water and hydrogen fromatmosphereVolcanismCooling of surfaceFaint young Sun?Glaciation?HeatMeteor bombardment and impactsLightningUV radiationHot oceans followed each bombardmentAtmosphere: N2, CO2, CO, H2, NH3, CH4, HCNOcean chemistry: H2S, Fe2+, heavy metals4.2Bombardment ceased (?)4.0RNA world, iron/sulfur worldLast universal common ancestor3.8Anoxygenic photosynthesis3.5–3.4Fossils resembling bacterial filaments on stromatolite microbial mats2.7Biomarker for cyanobacteriaBiomarker for primitive eukaryotesBanded iron geologic formations2.4Signs of oxygen at low concentration in atmosphereRed bed geologic formationsOxygen in atmosphere ~1%1.4Nucleated eukaryotic algaeOzone shieldOxygen in atmosphere ~21%0.60.4Cambrian explosion of eukaryotic diversity0.1Dinosaurs, higher plants, mammalsThe influence of ancient atmospheres upon surface conditions was critical. Abundances of greenhouse and other gases (especially CO2, NH3, H2O, CO, CH4, HCN, N2) were probably highly dynamic. In combination with variations in solar radiation, atmospheric conditions may have contributed to periods of high surface temperatures (~100°C) that perhaps alternated with low–temperature (glaciated) periods. Clearly, conditions on prebiotic Earth were turbulent characterized by fluctuating temperatures, aqueous reactions with magma, input of materials from meteorites (including organic carbon), electrical discharges from the atmosphere, and reduced (nonoxidizing) gases in the atmosphere.
Table 2.2 Scientific tools providing information about Earth history and evolution
DisciplineToolInsightsGeologyGlobal surveys of terrestrial and oceanic rocksSedimentary, igneous, and metamorphic formations reveal tectonic and other processes governing Earth's evolutionNuclear chemistryRadioisotopic datingAges of rocks, minerals, and their components are revealedPaleontologyFossil recordOrganism structures preserved in stratified sediments provide records of evolutionAnalytical chemistry of biomarkersAnalytical determination of biomolecules via chromatography and mass spectrometryMolecular remnants of biomolecules (membranes, pigments, cell walls, etc.)document ancient biotaAnalytical chemistry of isotopic ratiosIsotope ratio mass spectrometryEnzyme reactions favor substrate molecules composed of lighter atoms. Biomass assimilates the lighter isotope and the remaining isotopic pool becomes “heavier” for a given processExperimental biochemistryModel systems that simulate ancient EarthDiscovery of precursors of cellular structures and their self–assembling propertiesMolecular phylogenySequencing and analysis of informational biomoleculesAlignment of sequences from DNA, proteins,and other molecules allow evolutionary inferences to be drawn, especially regarding the three domains of lifeMineralogy and geochemistryX-ray diffraction and wetchemical analysis of rocksChemical reactions and reactants of past ages can be inferred from the composition and oxidation/reduction status of ancient sedimentsBiochemistryComparative biochemistry of cellular materialsTrends in evolutionary relatedness among and between members of Bacteria, Archaea, and Eukarya2.3 DID LIFE REACH EARTH FROM MARS?
There is a general consensus that stable isotopic ratios (see Tables 2.1, 2.2 and Box 2.2) in graphite isolated from the Isua supracrustal belt (West Greenland; see Figure 2.1
