Chapter
I. INTRODUCTION: THE RATIONALE
Chapter 1 Biotechnology, the Art of Exploiting Biology
THE IMPACT OF BIOTECHNOLOGY AND ITS CONTRIBUTION TO SUSTAINABLE INDUSTRY
BIOPROSPECTING: SCOPE AND ISSUES
II. MICROBIAL DIVERSITY: THE RESOURCE
Chapter 2 An Overview of Biodiversity—Estimating the Scale
Chapter 3 Defining Microbial Diversity—the Species Concept for Prokaryotic and Eukaryotic Microorganisms
WE (TAXONOMISTS) ARE NOT ALONE . . .
WHAT IS A SPECIES, OR WHAT CAN WE REGARD AS A SPECIES?
THE SPECIES CONCEPT FOR MICROSCOPIC EUKARYOTES
THE SPECIES CONCEPT FOR PROKARYOTES
Chapter 4 Speciation and Bacterial Phylospecies
SPECIATION IN ANIMALS AND PLANTS
BACTERIAL SPECIES CONCEPT
SPECIFIC RECOMMENDATION: THE PHYLOSPECIES
ENVIRONMENTAL (OR EXTRINSIC) FACTORS
FINAL COMMENTS AND RECOMMENDATIONS
Chapter 5 Approaches to Identification
APPROACHES TO IDENTIFICATION
NUCLEIC-ACID-BASED IDENTIFICATION
TECHNIQUES FOR EXAMINING PROTEINS
METHODS BASED ON CELL COMPOSITION
METHODS BASED ON PHYSIOLOGY
Chapter 6 Eukaryotic Diversity—a Synoptic View
IIΙ. MICROBIAL ECOLOGY: THE KEY TO DISCOVERY
Chapter 7 How To Look, Where To Look
Chapter 8 Culture-Dependent Microbiology
TRADITIONAL APPROACHES TO STUDYING MICROBIAL DIVERSITY
THE NEED FOR MORE PURE CULTURES TO STUDY DIVERSITY
MEDIA AND DETECTING THE TARGET BACTERIA
ENRICHMENT AND MICROMANIPULATION
Chapter 9 Culture-Independent Microbiology
WHY ARE CULTIVATION-INDEPENDENT TECHNIQUES NEEDED?
NUCLEIC ACID EXTRACTION FROM ENVIRONMENTAL SAMPLES
RNA EXTRACTION FROM ENVIRONMENTAL MATRICES
MOLECULAR ANALYSIS OF NUCLEIC ACIDS OBTAINED FROM ENVIRONMENTAL SAMPLES
ATTEMPTS TO LINK MICROBIAL COMMUNITY STRUCTURE WITH FUNCTION
CULTIVATION-INDEPENDENT STUDY OF THE HORIZONTAL GENE POOL
Chapter 10 Resuscitation of "Uncultured" Microorganisms
LOSS OF CULTURABILITY IN LABORATORY CULTURES—BASIC EXPERIMENTAL ISSUES
RPF: A BACTERIAL CYTOKINE FAMILY AND ITS BIOLOGY
RESUSCITABILITY OF BACTERIA TAKEN FROM ENVIRONMENTAL SAMPLES
Chapter 11 Soils—the Metagenomics Approach
THE HISTORY OF SOIL BIOLOGY
SOIL BIOLOGY AND THE ORIGINS OF METAGENOMICS
METAGENOMICS AS AN EXPERIMENTAL STRATEGY
FUNCTIONAL DIVERSITY IN SOIL
LINKING PHYLOGENY AND FUNCTION
BIOLOGICAL INSIGHTS INTO THE SOIL FROM METAGENOMICS
CHALLENGES AND LIMITATIONS IN METAGENOMIC ANALYSIS
FUTURE DIRECTIONS IN METAGENOMICS
Chapter 12 Deep Biospheres
MARINE SEDIMENTS AND ROCKS
PETROLEUM AND COAL RESERVOIRS
SIGNIFICANCE OF T H E DEEP BIOSPHERE
Chapter 13 Earth's Icy Biosphere
COLD EXTRA TERRESTRIAL LIFE?
EVOLUTION OF LIFE ON A FROZEN EARTH
PERMANENT ANTARCTIC LAKE ICE
EVIDENCE FOR COLD-ADAPTED MICROBIAL SPECIES
Chapter 14 Extremophiles: pH, Temperature, and Salinity
MICROORGANISMS LIVING AT EXTREME PH
MICROORGANISMS GROWING AROUND THE FREEZING POINT OF WATER
MICROORGANISMS GROWING AROUND THE BOILING POINT OF WATER
MICROORGANISMS GROWING AT EXTREME SALINITY
BIOCATALYSIS UNDER EXTREME CONDITIONS
Chapter 15 Extremophiles: Pressure
PHYSIOLOGICAL EFFECTS OF HIGH PRESSURE
THE ROLE OF MEMBRANE PROTEINS UNDER PRESSURE CONDITIONS
TRANSCRIPTIONAL REGULATION UNDER PRESSURE CONDITIONS
Chapter 16 Life in Extremely Dilute Environments:the Major Role of Oligobacteria
ACTIVITY CONTROL BY SUBSTRATE CONCENTRATION
Chapter 17 Anaerobes: the Sulfate-Reducing Bacteria as an Example of Metabolic Diversity†
BIOENERGETIC MECHANISMS OF DISSIMILATORY SULFATE REDUCTION
OTHER PROCESSES OF ENERGY CONSERVATION BY SULFATE REDUCERS
METAL REDUCTION BY DISSIMILATORY SULFATE REDUCERS
Chapter 18 Microbes from Marine Sponges: A Treasure Trove of Biodiversity for Natural Products Discovery
DIVERSITY OF MICROBES ASSOCIATED WITH SPONGES
MICROBIAL DIVERSITY IN SPONGES AS A RESOURCE FOR NATURAL PRODUCTS DISCOVERY
PRODUCTION OF BIOACTIVE COMPOUNDS BY SPONGE-ASSOCIATED MICROBES
MICROBIAL SYMBIONTS OF SPONGES AND NATURAL PRODUCTS DISCOVERY
MICROBIOLOGICAL STUDIES OF MANZAMINE-CONTAINING SPONGES
SYMBIONTS FROM OTHER MARINE INVERTEBRATES
SPONGE HEALTH AND AQUACULTURE
Chapter 19 Invertebrates—Insects
MICROBIAL ENDOSYMBIONTS OF INSECTS (EXTRACELLULAR)
MICROBIAL ENDOSYMBIONTS OF INSECTS (INTRACELLULAR)
BIOPROSPECTING WITHIN MICROBIAL SYMBIONTS OF INSECTS
Chapter 20 Microbial Symbioses with Plants
WHAT ARE PLANT-MICROBE SYMBIOSES?
DIVERSITY WITHIN PROKARYOTIC SYMBIOSES
DIVERSITY WITHIN EUKARYOTIC SYMBIOSES
PROSPECTS FOR EXPLOITATION
IV. BIOGEOGRAPHY AND MAPPING MICROBIAL DIVERSITY
Chapter 21 Ubiquitous Dispersal of Free-Living Microorganisms
THE KEY ROLE OF ABSOLUTE ABUNDANCE
EVIDENCE FOR UBIQUITOUS DISPERSAL
Chapter 22 Microbial Endemism and Biogeography
THE MICROBIAL BIOGEOGRAPHY DEBATE
ARE MICROBIAL EUKARYOTES REALLY COSMOPOLITAN, OR DO WE NEED A BETTER MAGNIFYING GLASS?
MANY PROKARYOTIC GENERA ARE COSMOPOLITAN
NARROWING THE FOCUS: THE GENOME AND ORGANISM SURROUNDING THE 16S RRNA GENE
CONCLUSIONS AND FUTURE DIRECTIONS
Chapter 23 Mapping Microbial Biodiversity Case Study: The Yellowstone National Park Microbial Database and Map Server
V. THE PARADIGM SHIFT: BIOINFORMATICS
Chapter 24 The Paradigm Shift in Microbial Prospecting
INTEGRATION AND INTEROPERABILITY
WHOLE GENOME SEQUENCING AND ANALYSIS
TOOLS FOR COMPARATIVE GENOME ANALYSIS
MICROBIAL GENOMICS: INCREASING OUR UNDERSTANDING OF EVOLUTION
FUNCTIONAL GENOME ANALYSIS OF MICROBIAL SPECIES
GENOMICS AS A TOOL TO UNDERSTAND UNCULTURABLE SPECIES
Chapter 26 Bacterial Proteomics
EXPERIMENTAL APPROACHES TO PROTEOME CHARACTERIZATION
MICROBIAL TYPING AT THE LEVEL OF THE PROTEOME
INVESTIGATIONS OF BACTERIAL PATHOGENESIS AT THE LEVEL OF THE PROTEOME
DEVELOPMENT OF THERAPEUTIC STRATEGIES THROUGH PROTEOMICS
PHENOMIC MEASUREMENT TOOLS
PREDICTING AND ANALYZING PHENOMIC DATA
HOW WILL PHENOMICS IMPACT BIOTECHNOLOGY?
Chapter 28 Phylogeny and Functionality: Taxonomy as a Roadmap to Genes
TAXONOMY AS A ROADMAP TO GENES FOR BIOPROSPECTING
TAXONOMY IS NOT PHYLOGENY
VI. PROSPECTING: THE TARGETS
Chapter 29 Sectors and Markets
BIOMATERIALS AND BIOMIMETICS
Chapter 30 Screening for Bioactivity
CLASSICAL ANTIBACTERIAL ASSAYS
CLASSICAL ANTIFUNGAL ASSAYS
ENZYME ENHIBITITORY ASSAYS
Chapter 31 Antimicrobials
NEED FOR NEW NATURAL PRODUCT ANTIBIOTICS
CHEMICAL DIVERSITY VERSUS BIOLOGICAL DIVERSITY
BACTERIAL DIVERSITY WITH RESPECT TO NATURAL PRODUCT ANTIBIOTICS
FUNGAL DIVERSITY WITH RESPECT TO NATURAL PRODUCT ANTIBIOTICS
OTHER MICROORGANISM SOURCES OF NATURAL PRODUCTS
SOURCES FOR FUTURE ANTIBACTERIAL ANTIBIOTICS
SOURCES FOR FUTURE ANTIFUNGAL ANTIBIOTICS
SOURCES FOR FUTURE ANTITUMOR ANTIBIOTICS
EPILOGUE: "WHAT YOU SEEK IS WHAT YOU FIND"
Chapter 32 Pharmacologically Active Agents of Microbial Origin
PHARMACOLOGICAL AGENTS AND IMPORTANCE OF MICROBIAL PRODUCTS
HIGH-THROUGHPUT SCREENING ASSAYS AND MICROBIAL PRODUCT DIVERSITY
PHARMACOLOGICALLY ACTIVE MICROBIAL PRODUCTS
CONCLUSIONS, TRENDS, AND PROSPECTS
Chapter 33 Bioprospecting for Industrial Enzymes: Importance of Integrated Technology Platforms for Successful Biocatalyst Development
THE NEEDLE IN THE HAYSTACK: FUNCTIONAL ASSAYS ARE APPLIED IN ITERATIVE SCREENING CYCLES FOR SELECTION OF THE BEST CANDIDATES
INFINITE BIOLOGICAL DIVERSITY IS A NATURAL LIBRARY FOR BIOPROSPECTING OF INDUSTRIAL ENZYMES
Chapter 34 Plant Growth-Promoting Agents
BIOTREATMENT—SOME GENERALIZATIONS
BIOTREATMENT—PRACTICALITYIN MOTION
BIOTREATMENT—SOME NOVELBIODIVERSITY DISCOVERED
BIOTREATMENT—A DETAILED CASE STUDY
Chapter 36 Bioprospecting Novel Antifoulants andAnti-Biofilm Agents from Microbes
MODULATION OF SURFACE COLONIZATION BY BACTERIA
VII. CONSERVATION OF MICROBIAL GENE POOLS
Chapter 37 Extinction and the Loss of Evolutionary History
THE LOSS OF BIODIVERSITY AND MASS EXTINCTIONS
Chapter 38 What Is the Evidence for the Loss of Microbial Diversity?
ANTHROPOGENIC ACTIVITIES CAUSING REDUCTIONS OF MICROBIAL SPECIES RICHNESS AND DIVERSITY
ANTHROPOGENIC ACTIVITIES THAT HAD A VARIABLE OR UNDETECTABLE EFFECT ON MICROBIAL SPECIES RICHNESS AND DIVERSITY
ANTHROPOGENIC ACTIVITIES LEADING TO AN INCREASE IN MICROBIAL DIVERSITY
DOES MICROBIAL SPECIES LOSS MATTER?
CONCLUSIONS AND FUTURE RESEARCH
VIII. CONVENTION ON BIOLOGICAL DIVERSITY: IMPLICATIONS FOR MICROBIAL PROSPECTING
Chapter 39 The Convention on Biological Diversity and Benefit Sharing
ACCESS TO GENETIC RESOURCES AND BENEFIT SHARING IN THE CBD AND NATIONAL ACCESS LEGISLATION
THE MOVE TO FAIRER PARTNERSHIPS
BENEFIT SHARING IN PRACTICE
Chapter 40 The Historical Context of Present Bioprospecting—Four Cases
BUSY LIZZIE AND SAINTPAULIA: TWO CASES OF COLONIAL BIOPROSPECTING
THE PERIWINKLE AND THE "HARDANGERVIDDA FUNGUS": TWO CASES OF POSTWAR BIOPROSPECTING
STRONG CLAIMS—BUT OFTEN WEAK DATA
Chapter 41 Biodiversity Prospecting: The INBio Experience
RESEARCH COLLABORATIVE AGREEMENTS
MICROBIAL BIOPROSPECTING AGREEMENTS AT INBIO-A SHORT REVIEW
ACHIEVEMENTS OF BIOPROSPECTING—THE EXPERIENCE OF INBio
Chapter 42 Contracts for Bioprospecting: the Yellowstone National Park Experience
YELLOWSTONE BIOPROSPECTING AND Taq POLYMERASE
THE DIVERSA COOPERATIVE RESEARCH AND DEVELOPMENT AGREEMENT
LEGAL CHALLENGES TO THE CRADA
THE CURRENT STATE OF BIOPROSPECTINGIN THE U.S. NATIONAL PARKS
AN EARLY EVALUATION OFBIOPROSPECTING IN U.S. NATIONAL PARKS
Chapter 43 Natural Products Research Partnerships with Multiple Objectives in Global Biodiversity Hot Spots: Nine Years of the International Cooperative Biodiversity Groups Program
Chapter 44 The Value of Biodiversity
THE INEVITABILITY OF VALUING BIODIVERSITY
THE EQUATION OF WELL-BEING
THE ECONOMIC BENEFITS OF BIODIVERSITY
BIODIVERSITY, INFORMATION, AND IRREVERSIBILITY
ECONOMIC VALUATION OF
BIODIVERSITY IN PRACTICE
Microbial Diversity and Bioprospecting
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