Soil microbiology, ecology, and biochemistry

Front cover......Page 1
Title page......Page 4
Copyright page......Page 5
Table of contents......Page 6
Contributors......Page 18
Preface......Page 20
Part I BACKGROUND......Page 22
GENERAL HISTORY AND SCOPE......Page 24
SOIL MICROBIOLOGY......Page 26
SOIL ECOLOGY......Page 31
SOIL BIOCHEMISTRY......Page 34
IN PERSPECTIVE......Page 40
REFERENCES AND SUGGESTED READING......Page 42
INTRODUCTION......Page 46
SOIL GENESIS AND FORMATION OF THE SOIL HABITAT......Page 47
PHYSICAL ASPECTS OF SOIL......Page 50
SOIL HABITAT SCALE AND OBSERVATION......Page 54
REFERENCES AND SUGGESTED READING......Page 70
Part II SOIL BIOTA......Page 72
INTRODUCTION......Page 74
SCALE OF INVESTIGATIONS AND COLLECTION OF SAMPLES......Page 75
STORAGE AND PRETREATMENT OF SAMPLES......Page 77
MICROBIAL BIOMASS......Page 78
SIGNATURE MOLECULES AS A MEASURE OF MICROBIAL BIOMASS AND MICROBIAL COMMUNITY STRUCTURE......Page 80
PHYSIOLOGICAL ANALYSES......Page 86
ACTIVITIES AND LOCATIONS OF ENZYMES......Page 93
FUNCTIONAL DIVERSITY......Page 98
REFERENCES AND SUGGESTED READING......Page 101
INTRODUCTION......Page 106
TYPES AND STRUCTURES OF NUCLEIC ACIDS......Page 107
USE OF NUCLEIC ACID ANALYSES FOR SOIL ECOLOGY STUDIES......Page 109
DIRECT MOLECULAR ANALYSIS OF SOIL BIOTA......Page 111
BIOSENSORS AND MARKER GENE TECHNOLOGIES......Page 113
EXTRACTION OF NUCLEIC ACIDS (DNA/RNA)......Page 114
ANALYSIS OF NUCLEIC ACID EXTRACTS......Page 117
PARTIAL COMMUNITY ANALYSES - PCR-BASED ASSAYS......Page 125
LEVEL OF RESOLUTION......Page 133
OTHER FACTORS THAT MAY AFFECT MOLECULAR ANALYSES......Page 134
SUMMARY......Page 135
REFERENCES......Page 136
INTRODUCTION......Page 140
PHYLOGENY......Page 141
GENERAL FEATURES OF PROKARYOTES......Page 147
CELL STRUCTURE......Page 148
METABOLISM AND PHYSIOLOGY......Page 153
BIODEGRADATION CAPACITY......Page 159
DIFFERENTIATION, SECONDARY METABOLISM, AND ANTIBIOTIC PRODUCTION......Page 162
CONCLUSIONS......Page 163
REFERENCES AND GENERAL READING......Page 164
INTRODUCTION......Page 166
CLASSIFICATION, CHARACTERISTICS, AND ECOLOGICAL ROLES IN SOIL......Page 172
REFERENCES AND SUGGESTED READING......Page 179
INTRODUCTION......Page 184
THE MICROFAUNA......Page 187
ROTIFERA......Page 190
NEMATODA......Page 191
MICROARTHROPODS......Page 195
ENCHYTRAEIDS......Page 196
MACROFAUNA......Page 199
SUMMARY......Page 206
REFERENCES......Page 207
Part III CONCEPTS AND INTERACTIONS......Page 214
INTRODUCTION......Page 216
MECHANISMS THAT DRIVE COMMUNITY STRUCTURE......Page 218
ECOSYSTEM DYNAMICS......Page 239
CONCLUSION......Page 246
REFERENCES AND SUGGESTED READING......Page 247
INTRODUCTION......Page 252
METABOLIC CLASSIFICATIONS OF SOIL ORGANISMS......Page 254
EXAMPLES OF SOIL MICROBIAL TRANSFORMATIONS......Page 262
HOW CAN THE MICROBIAL CONTRIBUTIONS BE VIEWED IN A SIMPLIFIED AND UNIFIED CONCEPT?......Page 272
REFERENCES......Page 277
INTRODUCTION......Page 278
ROOTS AS AN INTERFACE FOR PLANT-MICROBIAL MUTUALISMS......Page 279
MYCORRHIZAL SYMBIOSES......Page 280
SYMBIOSES INVOLVING N-FIXING ORGANISMS......Page 288
INTERACTIONS AMONG MUTUALISTS......Page 291
INTERACTIONS WITH PATHOGENS......Page 293
IMPLICATIONS FOR PLANT POPULATIONS AND COMMUNITIES......Page 296
CHALLENGES IN THE STUDY OF INTERACTIONS......Page 297
CONCLUSIONS......Page 298
REFERENCES AND SUGGESTED READING......Page 300
INTRODUCTION......Page 304
GEOGRAPHICAL DIFFERENCES IN SOIL BIOTA......Page 306
ASSOCIATION OF SOIL ORGANISMS WITH PLANTS......Page 308
SPATIAL HETEROGENEITY OF SOIL ORGANISMS......Page 311
VERTICAL DISTRIBUTION WITHIN THE SOIL PROFILE......Page 313
MICROSCALE HETEROGENEITY IN MICROBIAL POPULATIONS......Page 317
REFERENCES AND SUGGESTED READING......Page 320
Part IV BIOCHEMISTRY AND BIOGEOCHEMISTRY......Page 322
INTRODUCTION......Page 324
LONG-TERM CARBON CYCLE......Page 325
THE SHORT-TERM C CYCLE......Page 328
ECOSYSTEM C CYCLING......Page 330
COMPOSITION AND TURNOVER OF C INPUTS TO SOIL......Page 333
SOIL ORGANIC MATTER......Page 350
QUANTITY AND DISTRIBUTION OF ORGANIC MATTER IN SOILS......Page 356
ROLE OF METHANE IN THE C CYCLE......Page 357
REFERENCES AND SUGGESTED READING......Page 358
INTRODUCTION......Page 362
NITROGEN MINERALIZATION AND IMMOBILIZATION......Page 364
NITRIFICATION......Page 368
DENITRIFICATION......Page 376
OTHER NITROGEN TRANSFORMATIONS IN SOIL......Page 380
NITROGEN MOVEMENT IN THE LANDSCAPE......Page 381
REFERENCES AND SUGGESTED READING......Page 383
GLOBAL N INPUTS......Page 386
BIOLOGICAL NITROGEN FIXATION......Page 388
FREE-LIVING N2-FIXING BACTERIA......Page 393
ASSOCIATIVE N2-FIXING BACTERIA......Page 394
PHOTOTROPHIC BACTERIA......Page 395
SYMBIOTIC N2-FIXING ASSOCIATIONS BETWEEN LEGUMES AND RHIZOBIA......Page 396
BIOTECHNOLOGY OF BNF......Page 406
REFERENCES AND SUGGESTED READING......Page 407
INTRODUCTION......Page 410
PHOSPHORUS......Page 412
SULFUR......Page 421
MICRONUTRIENTS AND TRACE METALS......Page 434
ENVIRONMENTAL SIGNIFICANCE OF P, S, AND METAL BIOGEOCHEMISTRY......Page 444
REFERENCES AND SUGGESTED READING......Page 451
INTRODUCTION......Page 454
REACTION KINETICS......Page 455
MODELING THE DYNAMICS OF DECOMPOSITION AND NUTRIENT TRANSFORMATIONS......Page 460
ESTABLISHING POOL SIZES AND KINETIC CONSTANTS......Page 480
MODEL SELECTION AND EVALUATION......Page 482
REFERENCES AND SUGGESTED READING......Page 485
Part V SOIL ORGANISMS: MAN AND NATURE......Page 490
INTRODUCTION......Page 492
CHANGING SOIL ORGANISM POPULATIONS AND PROCESSES......Page 494
ALTERNATIVE AGRICULTURAL MANAGEMENT......Page 501
THE POTENTIAL FOR MANAGING MICROORGANISMS AND THEIR PROCESSES......Page 508
CONCLUDING COMMENTS ON MICROBIAL ECOLOGY......Page 520
REFERENCES AND SUGGESTED READING......Page 521
INTRODUCTION......Page 524
SOIL COMMUNITY ECOLOGY - CONTROLS OVER POPULATION AND COMMUNITY DYNAMICS......Page 527
MICROBIAL LIFE AT THE MICROBIAL SCALE - THE MICROBIAL LANDSCAPE......Page 528
A WHOLE PROFILE PERSPECTIVE......Page 530
SCALING TO THE ECOSYSTEM......Page 531
APPLICATION......Page 532
REFERENCES......Page 533