Environmental Microbiology

From Genomes to Biogeochemistry

Eugene L. Madsen

• Publisher: Wiley-Blackwell
• Year: 2015
• ISBN:
  9781118439609
• Edition: 2
• Topic: Biowissenschaften
• Subtopic: Mikrobiologie

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.

1
Significance, History, and Challenges of Environmental Microbiology

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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.

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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

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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 to 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), ­contribute to one half of global primary production via photosynthesis in marine habitats (Azam and Malfatti, 2007), 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 organi...