《水处理生物学》课程教学资源（书籍文献）《Environmental Microbiology》书籍PDF电子书 From genomes to biogeochemistry（Eugene L. Madsen）.pdf_大学文库

viCONTENTS3.677Aplanetof complexmixtures inchemical disequilibrium3.7Athermodynamichierarchydescribingbiosphereselectivepressures,energy82sources,and biogeochemical reactions3.8Using the thermodynamic hierarchy of half reactions to predictbiogeochemical85reactions in timeand space953.9Overview of metabolism and the"logic of electron transport310Theflow of carbon and electrons in anaerobicfood chains:syntrophy97is the rule1003.11The diversity of lithotrophic reactions1064ASurveyof theEarth'sMicrobialHabitats1074.1Terrestrial biomes4.2109Soils: geographic features relevant to both vegetation and microorganisms4.3113Aquatichabitats1214.4Subsurfacehabitats:oceanicand terrestrial1314.5Defining the prokaryotic biosphere: where do prokaryotes occur on Earth?1354.6Life at the micron scale: an excursion into the microhabitat of soilmicroorganisms1404.7Extreme habitatsfor lifeand microbiological adaptations150Microbial Diversity:Who is Here and How do we Know?51515.1Defining cultured and uncultured microorganisms5.2Approaching a census: an introduction to the environmental microbiological155"toolbox"1585.3Criteria for census taking:recognition of distinctive microorganisms (species)5.4162Proceeding toward census taking and measures of microbial diversity5.5169The tree of life: our view of evolution's blueprint for biological diversity5.6A sampling of key traits of cultured microorganisms from domains Eukarya,172Bacteria,andArchaea5.7Placing the "uncultured majority" on the tree of life: what have189nonculture-based investigations revealed?5.8194Viruses:an overview of biology,ecology,and diversity5.9Microbial diversity illustrated by genomics,horizontal gene transfer,and199cell size6Generating and Interpreting Information in Environmental Microbiology:Methods208andtheirLimitations6.1209How do we know?2096.2Perspectives from a century of scholars and enrichment-culturing procedures2136.3Constraints onknowledge imposed by ecosystem complexity6.4Environmental microbiology's"Heisenberg uncertainty principle":model215systems andtheirrisks6.5Fieldwork:being sure sampling procedures are compatiblewith analyses217andgoals6.6223Blending and balancingdisciplines from fieldgeochemistryto pure cultures

3.6 A planet of complex mixtures in chemical disequilibrium 77 3.7 A thermodynamic hierarchy describing biosphere selective pressures, energy sources, and biogeochemical reactions 82 3.8 Using the thermodynamic hierarchy of half reactions to predict biogeochemical reactions in time and space 85 3.9 Overview of metabolism and the “logic of electron transport” 95 310 The flow of carbon and electrons in anaerobic food chains: syntrophy is the rule 97 3.11 The diversity of lithotrophic reactions 100 4 A Survey of the Earth’s Microbial Habitats 106 4.1 Terrestrial biomes 107 4.2 Soils: geographic features relevant to both vegetation and microorganisms 109 4.3 Aquatic habitats 113 4.4 Subsurface habitats: oceanic and terrestrial 121 4.5 Defining the prokaryotic biosphere: where do prokaryotes occur on Earth? 131 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 140 5 Microbial Diversity: Who is Here and How do we Know? 150 5.1 Defining cultured and uncultured microorganisms 151 5.2 Approaching a census: an introduction to the environmental microbiological “toolbox” 155 5.3 Criteria for census taking: recognition of distinctive microorganisms (species) 158 5.4 Proceeding toward census taking and measures of microbial diversity 162 5.5 The tree of life: our view of evolution’s blueprint for biological diversity 169 5.6 A sampling of key traits of cultured microorganisms from domains Eukarya, Bacteria, and Archaea 172 5.7 Placing the “uncultured majority” on the tree of life: what have nonculture-based investigations revealed? 189 5.8 Viruses: an overview of biology, ecology, and diversity 194 5.9 Microbial diversity illustrated by genomics, horizontal gene transfer, and cell size 199 6 Generating and Interpreting Information in Environmental Microbiology: Methods and their Limitations 208 6.1 How do we know? 209 6.2 Perspectives from a century of scholars and enrichment-culturing procedures 209 6.3 Constraints on knowledge imposed by ecosystem complexity 213 6.4 Environmental microbiology’s “Heisenberg uncertainty principle”: model systems and their risks 215 6.5 Fieldwork: being sure sampling procedures are compatible with analyses and goals 217 6.6 Blending and balancing disciplines from field geochemistry to pure cultures 223 vi CONTENTS 9781405136471_1_pre.qxd 1/15/08 9:21 Page vi

PrefaceOverthepast2oyears,environmentalmicrobiologyhasemergedfroma rather obscure, applied niche within microbiology to become a pro-minent, ground-breaking area of biology.Environmental microbiology'srise in scholarly stature cannot be simplyexplained.But onefactor wascertainly pivotal in bringing environmental microbiology into the ranksof other key biological disciplines.That factor was molecular techniques.Thanks largely to Dr.Norman Pace (in conjunction with his many stu-dents)and Gary Olson and Carl Woese,nucleicacid analysis proceduresbegan to flow into environmental microbiology in the mid-1980s.Subsequently,a long series of discoveries have flooded out of environ-mental microbiology.This two-way flow is constantly accelerating andthe discoveries increasingly strengthen the links between environmentalmicrobiology 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 presentingenvironmental microbiology as a coherent discipline to both undergrad-uate and graduate students at Cornell University.The undergraduate coursewas initially team-taught by Drs. Martin Alexander and William C.Ghiorse. Later, W. C. Ghiorse and I taught the course. Still later I wasthe sole instructor.Still laterI became instructor of an advanced gradu-ateversionofthecourse.The intended audience forthis textis upper-level undergraduates, graduate students,and established scientistsseekingto expand theirareas of expertise.Environmental microbiology is inherently multidisciplinary.It pro-vides license to learn manythings.Students in university courses willrebelifthesubjecttheyarelearningfailsto developinto a coherentbodyofknowledge.Thus,presenting environmental microbiology to students ina classroom settingbecomes a challenge.Howcan somanydisparateareasof science (e.g,analytical chemistry,geochemistry,soil science, limno-logy,publichealth,environmental engineering,ecology,physiology,biogeochemistry,evolution,molecularbiology,genomics)bepresentedasaunified bodyof information?This textbook ismy attempt to answer that question.Perfection is alwaysevasive.But Ihave used fivecore concepts (seeSectionl.l)that are

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 upperlevel 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 9781405136471_1_pre.qxd 1/15/08 9:21 Page viii

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. 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. 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 9781405136471_4_001.qxd 1/15/08 9:21 Page 1

2CHAPTERISIGNIFICANCE,HISTORY,ANDCHALLENGESOFENVIRONMENTALMICROBIOLOGYCore concept 3.There is a mechanistic series of linkages between ourplanet's habitat diversity and what is recorded in the genomes ofmicroorganisms found in the world today.Diversity in habitats is syn-onymouswithdiversityinselectivepressuresandresources.Whenoper-ated upon byforces of evolution,theresultismolecular,metabolic, andphysiological diversity found in extantmicroorganisms and recorded intheir genomes.Coreconcept4.Advancements in environmental microbiology dependupon convergent lines of independent evidence using many measurementprocedures. These include microscopy,biomarkers,model cultivatedmicroorganisms,molecularbiology,andgenomictechniques applied tolaboratory-and field-based investigations.Core concept5.Environmental microbiology isa dynamic,methods-limited discipline.Each methodologyused by environmental microbio-logists has its own setof strengths,weaknesses,and potential artifacts.As new methodologies deliver new types of information to environmentalmicrobiology,practitioners need a sound foundation that affords inter-pretation of the meaning and place of the incoming discoveries.I.2SYNOPSISOFTHESIGNIFICANCEOFENVIRONMENTALMICROBIOLOGYWith the formation of planet Earth 4.6 × 10°years ago, an uncharted seriesofphysical,chemical,biochemical,and (later)biological eventsbegantounfold. Many of these events were slow or random or improbableRegardless of the precise details of how life developed on Earth, (seeSections2.3-2.7), it is now clear thatfor~70% of life'shistory,prokar-yotes werethe sole or dominant lifeforms.Prokaryotes (Bacteria andArchaea)were (and remain)not just witnesses of geologic, atmospheric,geochemical, and climatic changes that have occurred over the eons.Prokaryotes arealso activeparticipants and causativeagentsofmanygeo-chemical reactions found in the geologic record.Admittedly,moderneukaryotes(especiallylandplants)havebeenmajorbiogeochemicalandecological players on planet Earth during the most recent1.4×1o°years.Nonetheless,today,as always,prokaryotes remain the"hostsof the planet.Prokaryotescomprise~60%ofthetotalbiomass(Whitmanetal.,1998;seeChapter4),accountforasmuchas6o%oftotalrespirationofsometerrestrial habitats (Velvis, 1997;Hanson et al.,2000),and also colonizea variety of Earth's habitats devoid of eukaryotic life due to topographic,climatic and geochemical extremes of elevation, depth,pressure,pH, salin-ity,heat, orlight.The Earth's habitats present complex gradients of environmental con-ditions that include variations in temperature, light, pH, pressure, salin-ity,and both inorganic and organic compounds.The inorganicmaterialsrange from elemental sulfur to ammonia,hydrogen gas, and methane and

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, methodslimited 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 2 CHAPTER I SIGNIFICANCE, HISTORY, AND CHALLENGES OF ENVIRONMENTAL MICROBIOLOGY 9781405136471_4_001.qxd 1/15/08 9:21 Page 2

3CHAPTERISIGNIFICANCE,HISTORY,ANDCHALLENGESOFENVIRONMENTAL MICROBIOLOGYTable l.1Microorganisms'unique combination of traits and their broad impact on the biosphereTraits ofmicroorganismsEcological consequences of traitsSmall sizeGeochemical cycling of elementsUbiquitous distribution throughout Earth's habitatsDetoxification of organic pollutantsHigh specific surface areasDetoxification of inorganic pollutantsPotentially high rate of metabolic activityRelease of essential limiting nutrients fromPhysiological responsivenessthe biomassin onegeneration to thenextGeneticmalleabilityMaintainingthe chemical compositionof soil,Potential rapid growth ratesediment, water, and atmosphere requiredUnrivaled nutritional diversityby other forms of lifeUnrivaled enzymatic diversitytheorganicmaterialsrangefrom celluloseto lignin,fats,proteins,lipids.nucleic acid, and humic substances (see Chapter 7).Each geochemical set-ting (e.g.,anaerobic peatlands, oceanic hydrothermal vents, soil humus,deep subsurface sediments) features its own set of resources that can bephysiologically exploited by microorganisms.The thermodynamicallygoverned interactions between these resources, their settings, micro-organismsthemselves,and3.6x1o°yearsof evolutionareprobablythesource of metabolic diversity of the microbial world.Microorganisms are the primary agents of geochemical change.Theirunique combination of traits (Table 1.1) cast microorganisms in the roleof recycling agents for thebiosphere.Enzymes accelerate reaction ratesbetween thermodynamicallyunstable substances.Perhaps themost eco-logically importanttypes of enzymatic reactions arethosethat catalyzeoxidation/reduction reactions between electron donors and electronacceptors.Theseallowmicroorganismstogeneratemetabolicenergy,sur-vive, and grow.Microorganisms procreate by carrying out complex,genetically regulated sequences of biosynthetic and assimilative intracel-lular processes. Each daughter cell has essentially the same macro-molecular and elemental composition as its parent.Thus, integratedmetabolism of all nutrients (e.g.,carbon, nitrogen, phosphorus, sulfur,oxygen,hydrogen,etc.)is implicitin microbial growth.Thisgrowthandsurvivalofmicroorganismsdrivesthegeochemicalcyclingoftheelements,detoxifies many contaminant organic and inorganic compounds, makesessential nutrients present in the biomass of one generation available tothe next, and maintains the conditionsrequired by other inhabitants ofthebiosphere(Table1.1).Processescarried outbymicroorganismsinsoilssediments,oceans,lakes,andgroundwaters haveamajorimpact on envir-onmental quality,agriculture,andglobal climatechange.Theseprocessesare also the basis for current and emerging biotechnologies with indus-trial and environmental applications (see Chapter 8).Table 1.2presents

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. 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 macromolecular 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 CHAPTER I SIGNIFICANCE, HISTORY, AND CHALLENGES OF ENVIRONMENTAL MICROBIOLOGY 3 Table 1.1 Microorganisms’ unique combination of traits and their broad impact on the biosphere Traits of microorganisms Small size Ubiquitous distribution throughout Earth’s habitats High specific surface areas Potentially high rate of metabolic activity Physiological responsiveness Genetic malleability Potential rapid growth rate Unrivaled nutritional diversity Unrivaled enzymatic diversity Ecological consequences of traits Geochemical cycling of elements Detoxification of organic pollutants Detoxification of inorganic pollutants Release of essential limiting nutrients from the biomass in one generation to the next Maintaining the chemical composition of soil, sediment, water, and atmosphere required by other forms of life 9781405136471_4_001.qxd 1/15/08 9:21 Page 3