BlackwellPublishingEnvironmentalMicrobiologyFrom genomes tobiogeochemistryEugene L.Madsen
ContentsPrefacevili11Significance,History,and Challenges of Environmental Microbiology11.1Core concepts can unify environmental microbiology21.2Synopsisofthesignificanceofenvironmentalmicrobiology61.3A brief historyof environmental microbiology101.4Complexity of our world121.5Many disciplinesand their integration232Formationof theBiosphere:KeyBiogeochemical andEvolutionaryEvents2.124Issues and methods in Earth's history and evolution242.2Formation of earlyplanetEarth2.326Did life reach Earth from Mars?292.4Plausible stages in thedevelopment of early life332.5Mineral surfaces:the early iron/sulfur world could have driven biosynthesis2.634Encapsulation:akeyto cellular life352.7A plausible definition of the tree of life's"last universal common ancestor362.8The rise of oxygen372.9Evidence for oxygen and cellular life in the sedimentary record382.10Theevolution of oxygenicphotosynthesis2.11Consequences of oxygenic photosynthesis: molecular oxygen in the atmosphere43and large pools of organic carbon2.12Eukaryotic evolution:endosymbiotic theoryand the blending of traits from45ArchaeaandBacteria523Physiological Ecology: Resource Exploitation by Microorganisms3.1The cause of physiological diversity:diverse habitats provide selective pressures53overevolutionarytime533.2Biological and evolutionary insights fromgenomics3.3Fundamentals of nutrition: carbon-and energy-source utilization provide a62foundation forphysiological ecology3.4Selective pressures: ecosystem nutrientfluxes regulate the physiological status64and composition ofmicrobial communities3.5Cellular responses to starvation:resting stages,environmental sensing circuits,69gene regulation, dormancy,and slow growth
Contents Preface viii 1 Significance, History, and Challenges of Environmental Microbiology 1 1.1 Core concepts can unify environmental microbiology 1 1.2 Synopsis of the significance of environmental microbiology 2 1.3 A brief history of environmental microbiology 6 1.4 Complexity of our world 10 1.5 Many disciplines and their integration 12 2 Formation of the Biosphere: Key Biogeochemical and Evolutionary Events 23 2.1 Issues and methods in Earth’s history and evolution 24 2.2 Formation of early planet Earth 24 2.3 Did life reach Earth from Mars? 26 2.4 Plausible stages in the development of early life 29 2.5 Mineral surfaces: the early iron/sulfur world could have driven biosynthesis 33 2.6 Encapsulation: a key to cellular life 34 2.7 A plausible definition of the tree of life’s “last universal common ancestor” 35 2.8 The rise of oxygen 36 2.9 Evidence for oxygen and cellular life in the sedimentary record 37 2.10 The evolution of oxygenic photosynthesis 38 2.11 Consequences of oxygenic photosynthesis: molecular oxygen in the atmosphere and large pools of organic carbon 43 2.12 Eukaryotic evolution: endosymbiotic theory and the blending of traits from Archaea and Bacteria 45 3 Physiological Ecology: Resource Exploitation by Microorganisms 52 3.1 The cause of physiological diversity: diverse habitats provide selective pressures over evolutionary time 53 3.2 Biological and evolutionary insights from genomics 53 3.3 Fundamentals of nutrition: carbon- and energy-source utilization provide a foundation for physiological ecology 62 3.4 Selective pressures: ecosystem nutrient fluxes regulate the physiological status and composition of microbial communities 64 3.5 Cellular responses to starvation: resting stages, environmental sensing circuits, gene regulation, dormancy, and slow growth 69 9781405136471_1_pre.qxd 1/15/08 9:21 Page v
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
viiCONTENTS6.7Overviewofmethodsfordeterminingthepositionandcomposition226ofmicrobialcommunities6.8Methods for determining in situ biogeochemical activities and when243they occur6.9245Metagenomics and related methods: procedures and insights6.10Discovering the organisms responsiblefor particular ecological processes:255linkingidentitywithactivity2811MicrobialBiogeochemistry:aGrand Synthesis2827.1Mineral connections:the roles of inorganic elements in lifeprocesses2867.2Greenhousegasesand lessons frombiogeochemical modeling7.3The"stuff of life:identifying the pools of biosphere materials whose293microbiologicaltransformationsdrivethebiogeochemicalcycles3137.4Elementalbiogeochemical cycles:conceptsandphysiologicalprocesses3297.5Cellularmechanismsof microbial biogeochemicalpathways3357.6Mass balance approachestoelementalcycles3468Special and Applied Topics in Environmental Microbiology8.1346Other organisms asmicrobial habitats:ecological relationships8.2363Microbial residents of plants and humans8.3373Biodegradation and bioremediation8.4399Biofilms4038.5Evolutionofcatabolicpathwaysfororganiccontaminants4108.6Environmental biotechnology:overview and eight case studies8.7423Antibioticresistance442FutureFrontiers in Environmental Microbiology4429.1The influence of systems biology on environmental microbiology4489.2Ecological niches and theirgenetic basis9.3453Concepts help define future progress in environmental microbiology460Glossary467Index
6.7 Overview of methods for determining the position and composition of microbial communities 226 6.8 Methods for determining in situ biogeochemical activities and when they occur 243 6.9 Metagenomics and related methods: procedures and insights 245 6.10 Discovering the organisms responsible for particular ecological processes: linking identity with activity 255 7 Microbial Biogeochemistry: a Grand Synthesis 281 7.1 Mineral connections: the roles of inorganic elements in life processes 282 7.2 Greenhouse gases and lessons from biogeochemical modeling 286 7.3 The “stuff of life”: identifying the pools of biosphere materials whose microbiological transformations drive the biogeochemical cycles 293 7.4 Elemental biogeochemical cycles: concepts and physiological processes 313 7.5 Cellular mechanisms of microbial biogeochemical pathways 329 7.6 Mass balance approaches to elemental cycles 335 8 Special and Applied Topics in Environmental Microbiology 346 8.1 Other organisms as microbial habitats: ecological relationships 346 8.2 Microbial residents of plants and humans 363 8.3 Biodegradation and bioremediation 373 8.4 Biofilms 399 8.5 Evolution of catabolic pathways for organic contaminants 403 8.6 Environmental biotechnology: overview and eight case studies 410 8.7 Antibiotic resistance 423 9 Future Frontiers in Environmental Microbiology 442 9.1 The influence of systems biology on environmental microbiology 442 9.2 Ecological niches and their genetic basis 448 9.3 Concepts help define future progress in environmental microbiology 453 Glossary 460 Index 467 CONTENTS vii 9781405136471_1_pre.qxd 1/15/08 9:21 Page vii
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