Soil Microbiology, Ecology and Biochemistry

by Eldor Paul (Editor), Serita Frey (Editor)

Overview

Soil Microbiology, Ecology, and Biochemistry, Fifth Edition addresses the increasingly important field of soil biota and their interactions in research and education. Soil biota are extremely important, and especially relevant to today’s societal questions related to global change, ecosystem sustainability, and food security in our ever-changing environment. Revised by a group of world-renowned authors in many institutions and disciplines, this book relates breakthroughs in knowledge in this important field, along with its history and future applications. This new edition provides readable, practical, impactful information for many applied and fundamental disciplines. There is no other available volume on the topics covered that also integrates the concepts in a way that makes them useful to a broad group of readers.

Product Details

ISBN-13:	9780128229415
Publisher:	Elsevier Science
Publication date:	12/12/2023
Edition description:	5th ed.
Pages:	576
Product dimensions:	7.50(w) x 9.25(h) x (d)

About the Author

Eldor A. Paul is a Senior Research Scientist at the Natural Resources Ecology Laboratory at Colorado State University, Fort Collins and Professor Emeritus at Michigan State University, East Lansing. During his time at Michigan State, he was professor of Soil Microbiology and Biochemistry, and Crop and Soil Sciences. He earned degrees from the University of Alberta and the University of Minnesota. His research focuses on the dynamics of soil organic matter and the microbial ecology of soil. Dr. Paul is a Fellow of ASA, SSSA, the Canadian Society of Soil Science, and the American Association for the Advancement of Science.

Serita Frey is a microbial ecologist with over 30 years of experience studying microbes in the environment. She received her Ph.D. in Ecology from Colorado State University and is currently a professor in the Department of Natural Resources and the Environment at the University of New Hampshire. Her research examines how environmental change is altering the structure and function of forest ecosystems, with an emphasis on soil microbial communities and nutrient cycling processes. She is specifically interested in how anthropogenic stressors (e.g., climate change, nitrogen deposition, invasive species) affect the composition and diversity of soil microbial communities and microbial-mediated carbon and nitrogen cycles.

Table of Contents

Contributors     XVII
Preface     XIX
Background
Soil Microbiology, Ecology and Biochemistry in Perspective   E. A. Paul
General History and Scope     3
Soil Microbiology     5
Soil Ecology     10
Soil Biochemistry     13
In Perspective     19
References and Suggested Reading     21
The Soil Habitat   R. P. Voroney
Introduction     25
Soil Genesis and Formation of the Soil Habitat     26
Soil Profile     29
Physical Aspects of Soil     29
Soil Texture     30
Soil Structure     32
Soil Habitat Scale and Observation     33
Scale of Soil Habitat     33
Pore Space     35
Soil Solution Chemistry     39
Soil pH     43
Soil Temperature     43
Soil Water Content     45
Environmental Factors, Temperature and Moisture Interactions     48
References and Suggested Reading     49
Soil Biota
Physiological and Biochemical Methods for Studying Soil Biota and Their Function   E. Kandeler
Introduction     53
Scale of Investigations and Collection of Samples     54
Storage and Pretreatment of Samples     56
Microbial Biomass     57
Chloroform Fumigation Incubation and Extraction Methods     57
Substrate-Induced Respiration     58
Isotopic Composition of Microbial Biomass     58
Signature Molecules as a Measure of Microbial Biomass and Microbial Community Structure     59
ATP as a Measure of Active Microbial Biomass     59
Microbial Membrane Components and Fatty Acids     60
Respiratory Quinones as a Measure of Structural Diversity     62
Ergosterol as a Measure of Fungal Biomass     63
Lipopolysaccharides, Glycoproteins, and Cell Walls     64
Growth Rates from Signature Molecules     65
Physiological Analyses     65
Culture-Based Studies     65
Isolation and Characterization of Specific Organisms     66
Soil Organic Matter Decomposition and Respiration     67
Nitrogen Mineralization     72
Activities and Locations of Enzymes     72
Spectrophotometric Methods     73
Fluorescence Methods     75
Techniques for Imaging the Location of Enzymes     77
Functional Diversity     77
References and Suggested Reading     80
Molecular Methods for Studying Soil Ecology   J. E. Thies
Introduction     85
Types and Structures of Nucleic Acids     86
Use of Nucleic Acid Analyses for Soil Ecology Studies     88
Direct Molecular Analysis of Soil Biota     90
Nucleic Acid Hybridization     90
Confocal Microscopy     91
Biosensors and Marker Gene Technologies     92
Extraction of Nucleic Acids (DNA/RNA)     93
Choosing between DNA and RNA for Soil Ecology Studies     96
Analysis of Nucleic Acid Extracts     96
DNA:DNA Reassociation Kinetics     96
Microarrays     98
Restriction Fragment Length Polymorphism (RFLP) Analysis     100
Cloning     101
DNA Sequencing     102
Stable Isotope Probing     102
Partial Community Analyses-PCR-Based Assays     104
Electrophoresis of Nucleic Acids     107
PCR Fingerprinting     107
Similarity Analyses     112
Level of Resolution     112
Other Factors That May Affect Molecular Analyses     113
Sample Handling     113
Soil Chemical Factors     113
Sampling Scale     114
Summary      114
References     115
The Prokaryotes   K. Killham   J. I. Prosser
Introduction     119
Phylogeny     120
Cultivated Organisms     120
Uncultivated Organisms     121
Phylogeny and Function     125
General Features of Prokaryotes     126
Cell Structure     127
Unicellular Growth Forms     127
Filamentous and Mycelial Growth     129
Cell Walls     129
Internal Structure     131
Motility     132
Metabolism and Physiology     132
Carbon and Energy Sources     132
Oxygen Requirements     133
Substrate Utilization     134
Autochthony and Zymogeny     136
Oligotrophy, Copiotrophy, and the R-K Continuum     137
Facultativeness     138
Biodegradation Capacity     138
Cellulose     138
Pollutants     139
Differentiation, Secondary Metabolism, and Antibiotic Production     141
Conclusions     142
References and General Reading     143
Fungi and Eukaryotic Algae   R. G. Thorn   M. D. J. Lynch
Introduction      145
Classification, Characteristics, and Ecological Roles in Soil     151
Fungus-like Protists     151
Fungi (Chytridiomycota, Glomeromycota, Zygomycota, Ascomycota, and Basidiomycota)     153
Eukaryotic Algae     156
References and Suggested Reading     158
Fauna: The Engine for Microbial Activity and Transport   D. C. Coleman   D. H. Wall
Introduction     163
The Microfauna     166
Methods for Extracting and Counting Protozoa     168
Impacts of Protozoa on Ecosystem Function     168
Distribution of Protozoa in Soil Profiles     169
Rotifera     169
Nematoda     170
Nematode Feeding Habits     170
Zones of Nematode Activity in Soil     173
Nematode Extraction Techniques     174
Microarthropods     174
Enchytraeids     175
Macrofauna     178
Macroarthropods     178
Importance of the Macroarthropods     179
Oligochaeta (Earthworms)     179
Formicidae (Ants)     183
Termitidae (Termites)     183
Summary     185
References     186
Concepts and Interactions
The Ecology of Soil Organisms   S. J. Morris   C. B. Blackwood
Introduction     195
Mechanisms That Drive Community Structure     197
Physiological Limits     198
Intraspecific Competition     199
Dispersal in Space and Time     203
Predicting Population Growth     204
Interspecific Competition     204
Direct Effects of Exploitation     207
Indirect Effects of Exploitation     209
Mutualisms     211
Abiotic Factors     211
Changes in Community Structure through Time and Space     212
Historical and Geographic Contingency     214
Hierarchical Community Assembly Rules     215
Ecosystem Dynamics     218
Energy Flow     219
Carbon, Nutrient, and Water Cycles     221
Emergent Properties     224
Conclusion     225
References and Suggested Reading     226
The Physiology and Biochemistry of Soil Organisms   W. B. McGill
Introduction     231
Metabolic Classifications of Soil Organisms     233
Electrons and ATP     234
Substrate-Level Phosphorylation     234
Electron Transport Phosphorylation      235
Overview of Mechanisms to Generate ATP and Reducing Equivalents     238
Examples of Soil Microbial Transformations     241
Nitrogen Fixation     241
Aerobic Chemolithotrophic Examples     242
Oxidation of Reduced C     245
How Can the Microbial Contributions Be Viewed in a Simplified and Unified Concept?     251
A Model of Interconnected Cycles of Electrons     252
The Anoxygenic Cycle     253
The Oxygenic Cycle     253
References     256
The Ecology of Plant-Microbial Mutualisms   J. Powell   J. Klironomos
Introduction     257
Roots as an Interface for Plant-Microbial Mutualisms     258
Mycorrhizal Symbioses     259
Symbioses Involving N-Fixing Organisms     267
Interactions among Mutualists     270
Interactions with Pathogens     272
Implications for Plant Populations and Communities     275
Challenges in the Study of Interactions     276
Conclusions     277
References and Suggested Reading     279
Spatial Distribution of Soil Organisms   S. D. Frey
Introduction     283
Geographical Differences in Soil Biota      285
Association of Soil Organisms with Plants     287
Spatial Heterogeneity of Soil Organisms     290
Vertical Distribution within the Soil Profile     292
Microscale Heterogeneity in Microbial Populations     296
References and Suggested Reading     299
Biochemistry and Biogeochemistry
Carbon Cycling and Formation of Soil Organic Matter   W. Horwath
Introduction     303
Long-Term Carbon Cycle     304
The Short-Term C Cycle     307
Ecosystem C Cycling     309
Composition and Turnover of C Inputs to Soil     312
Plant and Microbial Lipids     315
Starch     315
Hemicelluloses, Pectins, and Cellulose     317
Lignin     320
Other Plant Cell Wall Carbohydrates and Proteins     324
Plant Secondary Compounds     325
Roots and Root Exudates     325
Cell Walls of Microorganisms     327
Soil Organic Matter     329
Soil Organic Matter Formation     329
Classical Fractions of Soil Organic Matter     332
Physical Analysis of Soil Organic Matter Fractions     333
Structure of Soil Organic Matter     335
Quantity and Distribution of Organic Matter in Soils     335
Role of Methane in the C Cycle     336
Future Considerations     337
References and Suggested Reading     337
Nitrogen Transformations   G. P. Robertson   P. M. Groffman
Introduction     341
Nitrogen Mineralization and Immobilization     343
Nitrification     347
The Biochemistry of Autotrophic Nitrification     347
The Diversity of Autotrophic Nitrifiers     349
Heterotrophic Nitrification     352
Environmental Controls of Nitrification     353
Inhibition of Nitrification     355
Denitrification     355
Denitrifier Diversity     356
Environmental Controls of Denitrification     358
Other Nitrogen Transformations in Soil     359
Nitrogen Movement in the Landscape     360
References and Suggested Reading     362
Blological N Inputs   P. J. Bottomley   D. D. Myrold
Global N Inputs     365
Biological Nitrogen Fixation     367
Free-Living N[subscript 2]-Fixing Bacteria     372
Associative N[subscript 2]-Fixing Bacteria     373
Phototrophic Bacteria     374
Symbiotic N[subscript 2]-Fixing Associations between Legumes and Rhizobia     375
Formation of the Symbiosis     375
Rhizobial Nodulation Genes     378
Plant Nodulation Genes     380
Development of BNF and Nitrogen Assimilatory Processes in Nodules     381
Symbiotic Associations between Actinorhizal Plants and Frankia     383
Biotechnology of BNF     385
Acknowledgments     386
References and Suggested Reading     386
Soil Biogeochemical Cycling of Inorganic Nutrients and Metals   A. F. Plante
Introduction     389
Phosphorus     391
The Soil Phosphorus Cycle     391
Nature and Forms of Phosphorus in Soil     393
Biological Importance of Phosphorus     397
Microbial Transformations of Phosphorus     398
Sulfur     400
The Soil Sulfur Cycle     400
Nature and Forms of Sulfur in Soil     402
Biological Importance of Sulfur     406
Microbial Transformations of Sulfur     406
Micronutrients and Trace Metals     413
Micronutrient and Trace Metal Cycling in Soil     413
Nature and Forms in Soil     414
Biological Importance     415
Microbial Transformations     417
Environmental Significance of P, S, and Metal Biogeochemistry     423
Eutrophication     423
Acid Sulfate Soils     423
Acid Mine Drainage     424
Heavy Metal Mining Using Microbes     426
Microbial Corrosion of Buried Iron and Concrete Pipes     427
Conclusion: Microorganisms as Unifiers of Elemental Cycles in Soil     430
References and Suggested Reading     430
The Dynamics of Soil Organic Matter and Nutrient Cycling   A. F. Plante   W. J. Parton
Introduction     433
Reaction Kinetics     434
Zero-Order Reactions     434
First-Order Reactions     435
Enzymatic Kinetics     436
Microbial Growth     437
Modeling the Dynamics of Decomposition and Nutrient Transformations     439
Simple Models     441
Multicompartmental Models     443
Alternative SOM Models     453
Models of Non-C Nutrient Elements     454
Ecosystem Models: Interactions of Nutrient Cycling and SOM Dynamics     457
Establishing Pool Sizes and Kinetic Constants     459
Model Selection and Evaluation     461
References and Suggested Reading      464
Soil Organisms: Man and Nature
Management of Organisms and Their Processes in Soils   J. L. Smith   H. P. Collins
Introduction     471
Changing Soil Organism Populations and Processes     473
Tillage and Erosion     474
Rangeland and Forest Health     477
Alternative Agricultural Management     480
Organic Agriculture     480
Biodynamic Agriculture     482
Composting     483
Crop Rotations and Green Manures     486
The Potential for Managing Microorganisms and Their Processes     487
Management of Native and Introduced Microorganisms     487
Managing Microbial Populations as Agents of Biological Control     488
Control of Insects     490
Weed Control     492
Use of Synthetic and Natural Compounds to Modify Soil Communities or Functions     493
Manipulating Soil Populations for Bioremediation of Xenobiotics     495
Concluding Comments on Microbial Ecology     499
References and Suggested Reading     500
Soil Microbiology, Ecology, and Biochemistry for the 21st Century   J. Schimel
Introduction     503
Soil Community Ecology-Controls over Population and Community Dynamics      506
Microbial Life at the Microbial Scale-the Microbial Landscape     507
A Whole Profile Perspective     509
Scaling to the Ecosystem     510
Application     511
Conclusions     512
References     512
Index     515

What People are Saying About This

From the Publisher

This thoroughly updated and expanded edition is the classic teaching text for students studying soil organisms and their processes.

Editorial Reviews

"This is a comprehensive text for the study of soil ecology. It covers the subject in sufficient depth for an advanced undergraduate or post graduate course in soil microbiology and biochemistry...the reader soon begins to relate the discussions to plant health and fruit development. The topics are covered to a depth that addresses a wide range of readers, from those who wish an overview of the subject to those who need to know the fundamental microbiology or biochemistry. The 18 chapters are divded into five broad subject areas, starting with background and continuing through the soil biota, interactions, biochemistry, and concluding with the impact of human processes. There is little current appreciation of the impact of cultivation on soil ecosystems, thus we employ few strategies to manage these systems to our advantage. A book like this is food for though." —Gary Strachan, in FRUIT GROWER

From the Publisher