BIOLOGY OF PLANT LITTER DECOMPOSITION
PART I BACKGROUND SOIL MICROBIOLOGY, ECOLOGY AND BIOCHEMISTRY IN PERSPECTIVE GENERAL HISTORY AND SCOPE SOIL MICROBIOLOGY SOIL ECOLOGY SOIL BIOCHEMISTRY IN PERSPECTIVE REFERENCES AND SUGGESTED READING CONTENTS THE SOIL HABITAT INTRODUCTION SOIL GENESIS AND FORMATION OF THE SOIL HABITAT SOIL PRO?LE PHYSICAL ASPECTS OF SOIL SOIL TEXTURE SOIL STRUCTURE SOIL HABITAT SCALE AND OBSERVATION SCALE OF SOIL HABITAT PORE SPACE SOIL SOLUTION CHEMISTRY SOIL PH SOIL TEMPERATURE SOIL WATER CONTENT ENVIRONMENTAL FACTORS, TEMPERATURE AND MOISTURE INTERACTIONS PART II SOIL BIOTA PHYSIOLOGICAL AND BIOCHEMICAL METHODS FOR STUDYING SOIL BIOTA AND THEIR FUNCTION INTRODUCTION SCALE OF INVESTIGATIONS AND COLLECTION OF SAMPLES STORAGE AND PRETREATMENT OF SAMPLES MICROBIAL BIOMASS CHLOROFORM FUMIGATION INCUBATION AND EXTRACTION METHODS SUBSTRATE-INDUCED RESPIRATION ISOTOPIC COMPOSITION OF MICROBIAL BIOMASS SIGNATURE MOLECULES AS A MEASURE OF MICROBIAL BIOMASS AND MICROBIAL COMMUNITY STRUCTURE ATP AS A MEASURE OF ACTIVE MICROBIAL BIOMASS MICROBIAL MEMBRANE COMPONENTS AND FATTY ACIDS RESPIRATORY QUINONES AS A MEASURE OF STRUCTURAL DIVERSITY ERGOSTEROL AS A MEASURE OF FUNGAL BIOMASS LIPOPOLYSACCHARIDES, GLYCOPROTEINS, AND CELL WALLS GROWTH RATES FROM SIGNATURE MOLECULES PHYSIOLOGICAL ANALYSES CULTURE-BASED STUDIES ISOLATION AND CHARACTERIZATION OF SPECI?C ORGANISMS SOIL ORGANIC MATTER DECOMPOSITION AND RESPIRATION NITROGEN MINERALIZATION ACTIVITIES AND LOCATIONS OF ENZYMES SPECTROPHOTOMETRIC METHODS FLUORESCENCE METHODS TECHNIQUES FOR IMAGING THE LOCATION OF ENZYMES FUNCTIONAL DIVERSITY MOLECULAR METHODS FOR STUDYING SOIL ECOLOGY INTRODUCTION TYPES AND STRUCTURES OF NUCLEIC ACIDS USE OF NUCLEIC ACID ANALYSES FOR SOIL ECOLOGY STUDIES DIRECT MOLECULAR ANALYSIS OF SOIL BIOTA NUCLEIC ACID HYBRIDIZATION CONFOCAL MICROSCOPY BIOSENSORS AND MARKER GENE TECHNOLOGIES EXTRACTION OF NUCLEIC ACIDS (DNA/RNA) CHOOSING BETWEEN DNA AND RNA FOR SOIL ECOLOGY STUDIES ANALYSIS OF NUCLEIC ACID EXTRACTS DNA:DNA REASSOCIATION KINETICS MICROARRAYS RESTRICTION FRAGMENT LENGTH POLYMORPHISM (RFLP) ANALYSIS CLONING DNA SEQUENCING STABLE ISOTOPE PROBING PARTIAL COMMUNITY ANALYSES—PCR-BASED ASSAYS ELECTROPHORESIS OF NUCLEIC ACIDS PCR FINGERPRINTING SIMILARITY ANALYSES LEVEL OF RESOLUTION OTHER FACTORS THAT MAY AFFECT MOLECULAR ANALYSES SAMPLE HANDLING SOIL CHEMICAL FACTORS SAMPLING SCALE SUMMARY REFERENCES THE PROKARYOTES INTRODUCTION PHYLOGENY CULTIVATED ORGANISMS UNCULTIVATED ORGANISMS PHYLOGENY AND FUNCTION GENERAL FEATURES OF PROKARYOTES CELL STRUCTURE UNICELLULAR GROWTH FORMS FILAMENTOUS AND MYCELIAL GROWTH CELL WALLS INTERNAL STRUCTURE MOTILITY METABOLISM AND PHYSIOLOGY CARBON AND ENERGY SOURCES OXYGEN REQUIREMENTS SUBSTRATE UTILIZATION AUTOCHTHONY AND ZYMOGENY OLIGOTROPHY, COPIOTROPHY, AND THE R–K CONTINUUM FACULTATIVENESS BIODEGRADATION CAPACITY CELLULOSE POLLUTANTS DIFFERENTIATION, SECONDARY METABOLISM, AND ANTIBIOTIC PRODUCTION CONCLUSIONS REFERENCES AND GENERAL READING FUNGI AND EUKARYOTIC ALGAE INTRODUCTION CLASSI?CATION, CHARACTERISTICS, AND ECOLOGICAL ROLES IN SOIL FUNGUS-LIKE PROTISTS FUNGI (CHYTRIDIOMYCOTA, GLOMEROMYCOTA, ZYGOMYCOTA, ASCOMYCOTA, AND BASIDIOMYCOTA) EUKARYOTIC ALGAE FAUNA: THE ENGINE FOR MICROBIAL ACTIVITY AND TRANSPORT INTRODUCTION THE MICROFAUNA METHODS FOR EXTRACTING AND COUNTING PROTOZOA IMPACTS OF PROTOZOA ON ECOSYSTEM FUNCTION DISTRIBUTION OF PROTOZOA IN SOIL PRO?LES ROTIFERA NEMATODA NEMATODE FEEDING HABITS ZONES OF NEMATODE ACTIVITY IN SOIL NEMATODE EXTRACTION TECHNIQUES MICROARTHROPODS ENCHYTRAEIDS MACROFAUNA MACROARTHROPODS IMPORTANCE OF THE MACROARTHROPODS OLIGOCHAETA (EARTHWORMS) FORMICIDAE (ANTS) TERMITIDAE (TERMITES) PART III CONCEPTS AND INTERACTIONS THE ECOLOGY OF SOIL ORGANISMS INTRODUCTION MECHANISMS THAT DRIVE COMMUNITY STRUCTURE PHYSIOLOGICAL LIMITS INTRASPECI?C COMPETITION DISPERSAL IN SPACE AND TIME PREDICTING POPULATION GROWTH INTERSPECI?C COMPETITION DIRECT EFFECTS OF EXPLOITATION INDIRECT EFFECTS OF EXPLOITATION MUTUALISMS ABIOTIC FACTORS CHANGES IN COMMUNITY STRUCTURE THROUGH TIME AND SPACE HISTORICAL AND GEOGRAPHIC CONTINGENCY HIERARCHICAL COMMUNITY ASSEMBLY RULES ECOSYSTEM DYNAMICS ENERGY FLOW CARBON, NUTRIENT, AND WATER CYCLES EMERGENT PROPERTIES CONCLUSION THE PHYSIOLOGY AND BIOCHEMISTRY OF SOIL ORGANISMS INTRODUCTION METABOLIC CLASSI?CATIONS OF SOIL ORGANISMS ELECTRONS AND ATP SUBSTRATE-LEVEL PHOSPHORYLATION ELECTRON TRANSPORT PHOSPHORYLATION OVERVIEW OF MECHANISMS TO GENERATE ATP AND REDUCING EQUIVALENTS EXAMPLES OF SOIL MICROBIAL TRANSFORMATIONS NITROGEN FIXATION AEROBIC CHEMOLITHOTROPHIC EXAMPLES OXIDATION OF REDUCED C HOW CAN THE MICROBIAL CONTRIBUTIONS BE VIEWED IN A SIMPLI?ED AND UNI?ED CONCEPT? A MODEL OF INTERCONNECTED CYCLES OF ELECTRONS THE ANOXYGENIC CYCLE THE OXYGENIC CYCLE THE ECOLOGY OF PLANT–MICROBIAL MUTUALISMS INTRODUCTION ROOTS AS AN INTERFACE FOR PLANT–MICROBIAL MUTUALISMS MYCORRHIZAL SYMBIOSES SYMBIOSES INVOLVING N-FIXING ORGANISMS INTERACTIONS AMONG MUTUALISTS INTERACTIONS WITH PATHOGENS IMPLICATIONS FOR PLANT POPULATIONS AND COMMUNITIES CHALLENGES IN THE STUDY OF INTERACTIONS SPATIAL DISTRIBUTION OF SOIL ORGANISMS INTRODUCTION GEOGRAPHICAL DIFFERENCES IN SOIL BIOTA ASSOCIATION OF SOIL ORGANISMS WITH PLANTS SPATIAL HETEROGENEITY OF SOIL ORGANISMS VERTICAL DISTRIBUTION WITHIN THE SOIL PRO?LE MICROSCALE HETEROGENEITY IN MICROBIAL POPULATIONS PART IV BIOCHEMISTRY AND BIOGEOCHEMISTRY CARBON CYCLING AND FORMATION OF SOIL ORGANIC MATTER INTRODUCTION LONG-TERM CARBON CYCLE THE SHORT-TERM C CYCLE ECOSYSTEM C CYCLING COMPOSITION AND TURNOVER OF C INPUTS TO SOIL PLANT AND MICROBIAL LIPIDS STARCH HEMICELLULOSES, PECTINS, AND CELLULOSE LIGNIN OTHER PLANT CELL WALL CARBOHYDRATES AND PROTEINS PLANT SECONDARY COMPOUNDS ROOTS AND ROOT EXUDATES CELL WALLS OF MICROORGANISMS SOIL ORGANIC MATTER SOIL ORGANIC MATTER FORMATION CLASSICAL FRACTIONS OF SOIL ORGANIC MATTER PHYSICAL ANALYSIS OF SOIL ORGANIC MATTER FRACTIONS STRUCTURE OF SOIL ORGANIC MATTER QUANTITY AND DISTRIBUTION OF ORGANIC MATTER IN SOILS ROLE OF METHANE IN THE C CYCLE FUTURE CONSIDERATIONS NITROGEN TRANSFORMATIONS INTRODUCTION NITROGEN MINERALIZATION AND IMMOBILIZATION NITRI?CATION THE BIOCHEMISTRY OF AUTOTROPHIC NITRI?CATION THE DIVERSITY OF AUTOTROPHIC NITRI?ERS HETEROTROPHIC NITRI?CATION ENVIRONMENTAL CONTROLS OF NITRI?CATION INHIBITION OF NITRI?CATION DENITRI?CATION DENITRI?ER DIVERSITY ENVIRONMENTAL CONTROLS OF DENITRI?CATION OTHER NITROGEN TRANSFORMATIONS IN SOIL NITROGEN MOVEMENT IN THE LANDSCAPE BIOLOGICAL N INPUTS GLOBAL N INPUTS BIOLOGICAL NITROGEN FIXATION FREE-LIVING N2-FIXING BACTERIA ASSOCIATIVE N2-FIXING BACTERIA PHOTOTROPHIC BACTERIA SYMBIOTIC N2-FIXING ASSOCIATIONS BETWEEN LEGUMES AND RHIZOBIA FORMATION OF THE SYMBIOSIS RHIZOBIAL NODULATION GENES PLANT NODULATION GENES DEVELOPMENT OF BNF AND NITROGEN ASSIMILATORY PROCESSES IN NODULES SYMBIOTIC ASSOCIATIONS BETWEEN ACTINORHIZAL PLANTS AND FRANKIA BIOTECHNOLOGY OF BNF ACKNOWLEDGMENTS SOIL BIOGEOCHEMICAL CYCLING OF INORGANIC NUTRIENTS AND METALS INTRODUCTION PHOSPHORUS THE SOIL PHOSPHORUS CYCLE NATURE AND FORMS OF PHOSPHORUS IN SOIL BIOLOGICAL IMPORTANCE OF PHOSPHORUS MICROBIAL TRANSFORMATIONS OF PHOSPHORUS SULFUR THE SOIL SULFUR CYCLE NATURE AND FORMS OF SULFUR IN SOIL BIOLOGICAL IMPORTANCE OF SULFUR MICROBIAL TRANSFORMATIONS OF SULFUR MICRONUTRIENTS AND TRACE METALS MICRONUTRIENT AND TRACE METAL CYCLING IN SOIL NATURE AND FORMS IN SOIL BIOLOGICAL IMPORTANCE MICROBIAL TRANSFORMATIONS ENVIRONMENTAL SIGNI?CANCE OF P, S, AND METAL BIOGEOCHEMISTRY EUTROPHICATION ACID SULFATE SOILS ACID MINE DRAINAGE HEAVY METAL MINING USING MICROBES MICROBIAL CORROSION OF BURIED IRON AND CONCRETE PIPES CONCLUSION: MICROORGANISMS AS UNI?ERS OF ELEMENTAL CYCLES IN SOIL THE DYNAMICS OF SOIL ORGANIC MATTER AND NUTRIENT CYCLING INTRODUCTION REACTION KINETICS ZERO-ORDER REACTIONS FIRST-ORDER REACTIONS ENZYMATIC KINETICS MICROBIAL GROWTH MODELING THE DYNAMICS OF DECOMPOSITION AND NUTRIENT TRANSFORMATIONS SIMPLE MODELS MULTICOMPARTMENTAL MODELS ALTERNATIVE SOM MODELS MODELS OF NON-C NUTRIENT ELEMENTS ECOSYSTEM MODELS: INTERACTIONS OF NUTRIENT CYCLING AND SOM DYNAMICS ESTABLISHING POOL SIZES AND KINETIC CONSTANTS MODEL SELECTION AND EVALUATION PART V SOIL ORGANISMS: MAN AND NATURE MANAGEMENT OF ORGANISMS AND THEIR PROCESSES IN SOILS INTRODUCTION CHANGING SOIL ORGANISM POPULATIONS AND PROCESSES TILLAGE AND EROSION RANGELAND AND FOREST HEALTH ALTERNATIVE AGRICULTURAL MANAGEMENT ORGANIC AGRICULTURE BIODYNAMIC AGRICULTURE COMPOSTING CROP ROTATIONS AND GREEN MANURES THE POTENTIAL FOR MANAGING MICROORGANISMS AND THEIR PROCESSES MANAGEMENT OF NATIVE AND INTRODUCED MICROORGANISMS MANAGING MICROBIAL POPULATIONS AS AGENTS OF BIOLOGICAL CONTROL CONTROL OF INSECTS WEED CONTROL USE OF SYNTHETIC AND NATURAL COMPOUNDS TO MODIFY SOIL COMMUNITIES OR FUNCTIONS MANIPULATING SOIL POPULATIONS FOR BIOREMEDIATION OF XENOBIOTICS CONCLUDING COMMENTS ON MICROBIAL ECOLOGY SOIL MICROBIOLOGY, ECOLOGY, AND BIOCHEMISTRY FOR THE 21ST CENTURY INTRODUCTION SOIL COMMUNITY ECOLOGY—CONTROLS OVER POPULATION AND COMMUNITY DYNAMICS MICROBIAL LIFE AT THE MICROBIAL SCALE—THE MICROBIAL LANDSCAPE A WHOLE PRO?LE PERSPECTIVE SCALING TO THE ECOSYSTEM APPLICATION