The living soil is crucial to photosynthesis, biogeochemical cycles, global food production, climate change, biodiversity, and plant and animal health. In the past decade, scientists have made significant advances in soil microbiology research. While the basic principles are now better understood, knowledge has been forthcoming on the best available technologies and methods applied to researching soil microorganisms, their diversity, interactions, biochemistry, survival, gene expression, and their roles in global climate change, plant disease suppression and growth stimulation, and biogeochemical cycles. This knowledge can be applied to better predict the transformation of pollutants in soil and the activities of microbes in the rhizosphere. It will also assist us in fostering crop production in an era with an increasing human population and intensification of agriculture.
Following the tradition of its predecessors, Modern Soil Microbiology, Third Edition, is an indispensable source that supports graduate/undergraduate teaching for soil and environmental microbiologists in academia, as well as in government and industrial laboratories. It is a comprehensive collection of chapters on various aspects of soil microbiology, useful for all professionals working with soils. Compiled by internationally renowned educators and research scholars, this textbook contains key tables, figures, and photographs, supported by thousands of references to illustrate the depth of knowledge in soil microbiology.
FEATURES
- Fully updated and expanded to include new key chapters on historical developments, future applications, and soil viruses and proteins
- Discusses molecular methods applied to soil microbiology, diverse soil microorganisms, and global climate change
- Emphasizes the role of terrestrial microorganisms and cycles involved in climate change
- Details the latest molecular methods applied to soil microbiology research
- User-friendly for students, and containing numerous tables, figures, and illustrations to better understand the current knowledge in soil microbiology
Author(s): Jan Dirk van Elsas (ed.), Jack T. Trevors (ed.), Alexandre Soares Rosado (ed.), and Paolo Nannipieri (ed.)
Edition: 3rd edition
Publisher: Taylor & Francis
Year: 2019
Language: English
Commentary: CRC Press is an imprint of Taylor & Francis Group.
Pages: 472
City: Boca Raton
Tags: Soil microbiology; Molecular microbiology
Cover......Page 1
Half Title......Page 2
Title Page......Page 4
Copyright Page......Page 5
Contents......Page 6
Preface......Page 10
Editors......Page 12
Contributors......Page 14
SECTION I: Fundamental Chapters......Page 18
1.1 Introduction......Page 20
1.2.1 Introduction......Page 21
1.2.2 Spatial and Temporal Scales in Soil......Page 22
1.3.1 Water—The Essential Factor for Soil Life......Page 23
1.3.1.1 Definitions......Page 25
1.3.2 Soil as an Energy and Nutrient Source......Page 26
1.3.3 Soil Temperature......Page 28
1.3.5 Soil Atmosphere and Redox Potential......Page 31
1.3.6 Soil pH......Page 33
References......Page 35
2.1 Introduction......Page 38
2.2 Developments Examined by McLaren......Page 39
2.3.1 Intracellular Activities in Soil Microbiomes......Page 41
2.4 What Associative and Antagonistic Influences Exist among Soil Microflora and Fauna?......Page 42
2.5.1 The Importance of SOM......Page 43
2.6.1 The Processes That Determine the Role of C in Soil......Page 44
2.6.3 The Flow of Energy in Soil......Page 45
2.8 How Can One Modify Soil Populations and to What Ends?......Page 46
2.9 What Interrelationships Exist between Physicochemical Conditions in Soil and Microbial Activities?......Page 47
2.10 Conclusions and Perspectives......Page 48
References......Page 50
3.1 Introduction......Page 54
3.2 Sampling of the Soil Microbiome......Page 56
3.3 The Ubiquity of Soil Microbiomes and Their Structures......Page 57
3.4 Determinants of Soil Microbiome Characteristics......Page 58
3.5.2 The Tree of Life......Page 60
3.6 Does Soil Ecosystem Functioning Reflect Microbiome Structure?......Page 61
3.7 Ecological Resistance and Resilience in Soil Microbiomes......Page 62
3.8 Concluding Remarks......Page 63
References......Page 64
4.1 Introduction......Page 66
4.2.1 Growth Strategies......Page 67
4.2.2 Generalists versus Specialists......Page 68
4.3.1 Data from Traditional and Advanced Cultivation-Based Approaches......Page 71
4.3.2.2 Archaeal Diversity......Page 74
4.4.1 Physiological and Genetic Adaptations to Soil Conditions......Page 75
4.4.2 Physiological Response to Nutrient Limitation......Page 76
4.4.3 Implications for Survival of Bacterial Inoculants in Soil......Page 78
4.5 Concluding Remarks......Page 79
References......Page 80
Chapter 5 The Fungi in Soil......Page 82
5.2 Diversity of Fungi and Fungus-Like Organisms......Page 83
5.2.3 Glomeromycota......Page 85
5.2.6 Fungus-Like Organisms......Page 86
5.3 Taxonomy and Evolution......Page 87
5.4.2 Measurements of Fungal Activity......Page 88
5.5 Fungal Metabolites and Metabolism......Page 89
5.6 Fungal Saprotrophs—Litter Decomposition......Page 91
5.7 Fungal Parasites and Pathogens......Page 93
5.8.1 Arbuscular Mycorrhiza (AM)......Page 94
5.8.3 Ectomycorrhiza......Page 95
5.8.4 Orchid Mycorrhiza, Monotropid Mycorrhiza, and Mycoheterotrophs......Page 96
5.8.6 Lichens, Endophytes, and Other Types of Symbioses......Page 97
5.8.7 Functional Effects of Mycorrhizal Fungi......Page 98
5.9.1 Interactions with Bacteria......Page 99
5.9.3 Interactions with Soil Microfauna and Mesofauna......Page 100
5.11 Applications of Soil Fungi......Page 101
5.11.2 Bioremediation......Page 103
5.12 Conclusions......Page 104
References......Page 105
6.1 Introduction—Soil Viromes......Page 108
6.3.1 The Effect of Soil Habitat Structure on Virus–Host Interactions......Page 109
6.3.2 Soil Viromes—Mixed Communities of Agents Infecting Diverse Hosts......Page 110
6.4.1 Abundance......Page 112
6.4.2 Diversity......Page 114
6.5.1 Phages as Controllers of Host Population Densities......Page 117
6.6.1 Three Approaches to Soil Virome Studies......Page 118
6.6.2 Spatiotemporal Aspects of Virus–Host Interactions......Page 119
References......Page 120
7.1 Introduction......Page 122
7.2.1 Introduction of Genetic Changes through Random Mutation......Page 123
7.2.2 Introduction of Genetic Changes through Horizontal Transfer of Chromosomal DNA......Page 125
7.2.3 Introduction of Genetic Changes through Horizontal Transfer of Mobile Genetic Elements......Page 126
7.3.1 Natural Transformation in Soil......Page 127
7.3.2.1 Mechanisms and MGEs Involved......Page 128
7.3.2.2 Historical Overview of Studies on Conjugation in Soil......Page 129
7.3.2.3 Conjugation Occurs Preferentially in Soil Hot Spots and in Biofilms......Page 130
7.4 Methods Used to Study HGT in Soil......Page 131
7.4.1 Retrospective Identification of Horizontally Transferred DNA Sequences in Bacterial Genes or Genomes......Page 132
7.5 Population-Scale Considerations of HGT Events......Page 133
7.7 Concluding Remarks......Page 136
References......Page 137
8.1 Introduction......Page 142
8.2 Short Description of the Main Eukaryotic Groups......Page 143
8.4.1 Molecular Approaches......Page 146
8.5 Sexuality in Protists......Page 148
8.6 Protistan Feeding Modes......Page 150
8.7 Protists in the Soil Food Web......Page 152
8.8.1 Roles of Protists in Plant Nutrient Uptake......Page 154
Acknowledgments......Page 155
References......Page 156
Chapter 9 Microbial Interactions in Soil......Page 158
9.1.3 Interaction Studies Performed at Different Scales......Page 159
9.2.1 Microbial Assemblages, Microcolonies, and Biofilms......Page 160
9.2.2 Function-Driven Microbial Communities......Page 161
9.3.1 Molecular Sensing and Signaling......Page 162
9.3.2 Quorum Sensing (QS)—The Paradigm of Signaling between Microorganisms in Nature......Page 163
9.4.1 Concepts and Terms to Describe Microbial Interactive Systems......Page 165
9.4.2 Interactions Classified with Respect to Ecological Effects......Page 166
9.4.2.1 Mutualistic Interactions......Page 167
9.4.2.2 Antagonistic Interactions......Page 168
9.5.1 How Bacteria Interact with Fungi in Soil......Page 169
9.5.2 How Fungi “Cope” with Bacteria and Other Organisms in Soil......Page 171
9.5.4 Molecular Recognition Mechanisms in Interactions between Bacteria and Eukaryotes in Soil......Page 172
9.6.1 Protozoa as Predators of Bacteria......Page 173
9.6.2 Predatory Bdellovibrio......Page 174
9.7 Concluding Remarks......Page 175
References......Page 176
10.1 Introduction......Page 180
10.2.1 Non-vegetated Soil......Page 181
10.2.2.1 The Rhizosheath......Page 183
10.2.2.2 The Rhizoplane......Page 184
10.2.3 Root Endosphere......Page 185
10.4 Host Factors Shaping Root Microbiota......Page 186
10.4.1.2 Root-Mediated Lateral Patterns of Bacterial Communities......Page 187
10.4.3 The Plant Immune System......Page 188
10.5.2 Root Endophyte Competence......Page 189
10.6 Root Core Microbiome......Page 190
10.7.2 Pathogenic Bacteria......Page 191
References......Page 192
11.1 Introduction......Page 196
11.2 The Soil Carbon Cycle......Page 197
11.2.3 The Methane Cycle......Page 198
11.3 The Nitrogen Cycle......Page 199
11.3.1 Biological Nitrogen Fixation......Page 201
11.3.2 Nitrification......Page 202
11.3.3 Denitrification......Page 203
11.4.1 Phosphorus......Page 204
11.4.2 Sulfur......Page 205
11.5 Future Perspectives......Page 206
References......Page 207
SECTION II: Methods Chapters......Page 210
Chapter 12 Methods to Determine Bacterial Abundance, Localization, and General Metabolic Activity in Soil......Page 212
12.1 Introduction......Page 213
12.2.1.1 Extraction of DNA from Soil......Page 214
12.2.3 PCR-Based Detection of DNA Extracted from Soil......Page 216
12.2.3.1 Quantitative PCR......Page 217
12.2.3.2 Digital Droplet PCR......Page 218
12.3.1 Methods for Extraction of Bacterial Cells from Soil......Page 220
12.3.2.1 Epifluorescence Microscopy (EFM)......Page 221
12.3.2.2 Flow Cytometry......Page 222
12.3.3.2 Fluorescence In Situ Hybridization (FISH)......Page 223
12.3.3.4 ImmunoFluorescence (IF; Fluorescent Antibody) Methods......Page 224
12.3.4.1 The Concepts of Bacterial Viability and Activity......Page 225
12.3.4.2 Assays Determining Bacterial Viability......Page 226
12.4 Detection and Enumeration of Soil Bacteria by Cultivation-Dependent Methods......Page 227
12.5 Conclusions and Outlook......Page 228
References......Page 229
13.1 Introduction......Page 232
13.2.1.2 The Case of Fungi......Page 233
13.3 Soil Microbiome Data Analysis......Page 234
13.3.1 Initial Data Processing: From Raw Data to Operational Taxonomic Units......Page 235
13.3.2.1 Data Normalization......Page 236
13.3.3 Correlation Analysis......Page 237
13.4 Concluding Remarks......Page 239
References......Page 242
14.1 Introduction......Page 244
14.2 Principles of Soil Metagenomics......Page 245
14.3 Soil Microbiome DNA Isolation......Page 246
14.4.1 Direct Sequencing Techniques......Page 247
14.4.2 Key Considerations for Successful Metagenomics-Based Analysis of Soil......Page 248
14.4.4 Construction of Genomes from Metagenomes......Page 249
14.5 Targeted Gene Discovery and Bioprospecting......Page 250
14.5.1 Metagenome Libraries, Vectors, and Hosts......Page 252
14.5.2.2 Functional Screening......Page 253
14.6 Soil Metagenomics to Assess and Understand Microbial Ecology and Evolution......Page 254
14.7 Examples of Successful Metagenomics-Based Studies of Soils......Page 255
14.8 Commercialization of Activity-Based Metagenomic Products......Page 256
14.9 Future Contribution of Soil Metagenomics to Different Scientific Aims......Page 257
References......Page 258
15.1.1 Microbial RNA—An Activity Parameter for Soil Microbial Communities?......Page 262
15.1.2 Challenges in Transcript Analyses......Page 263
15.2.1 Sampling and Storage of Samples......Page 264
15.2.2 Extraction Protocols......Page 265
15.2.3 Purification......Page 266
15.2.5 Reverse Transcription......Page 267
15.3.1 PCR-Based Approaches......Page 268
15.3.3 Metatranscriptomes......Page 269
15.4 Conclusions and Outlook......Page 270
References......Page 272
16.1 Introduction......Page 274
16.2.1 Definitions and Developments......Page 275
16.2.2 Approaches in Environmental Proteomics......Page 276
16.3.1 Proteomics Studies in Model Soil and Laboratory Systems......Page 277
16.3.2 Proteomics Studies in Soil: The State of the Art and the Technical Challenges......Page 278
16.3.3 Conceptual Challenges: Protein Distribution in the Soil Matrix, Soil Proteomics, and Soil Metaproteomics......Page 281
16.4 Conclusions and Prospects for Future Research......Page 282
References......Page 284
17.1.1 What Is Stable Isotope Probing (SIP)?......Page 286
17.1.3 What Are the Typical Applications of SIP in Soil?......Page 287
17.2.1.1 Choice of Target Molecule......Page 289
17.2.1.3 Choice of Incubation Technique......Page 302
17.2.2 Carbon Cycling Studies......Page 304
17.2.3 Nitrogen Cycling Studies......Page 305
17.2.5 PLFA-SIP in Soil Research......Page 316
17.3 Analyzing SIP High-Throughput Sequencing Data......Page 317
17.5 Conclusion and Outlook......Page 318
References......Page 319
18.1 Introduction—The Great Plate Count Anomaly......Page 324
18.2 Uncultured Bacteria—The Unseen Majority......Page 325
18.3.1 Strategies in the Development of Growth Media......Page 326
18.3.2 The Use of Different Media and Growth Conditions......Page 329
18.3.2.3 Addition of Micronutrients and Use of Different Atmospheric Compositions......Page 330
18.4 How Far Have We Come with the Novel Isolation Approaches?......Page 331
18.5 Outlook and Prospects......Page 332
References......Page 333
19.1 Introduction......Page 336
19.2.1 Variables and Measurement Scales......Page 337
19.2.2 Descriptive Statistics......Page 339
19.2.3 Graphical Descriptions......Page 342
19.3 Hypothesis Testing......Page 343
19.3.2 Null and Alternative Hypotheses......Page 346
19.3.3 Parametric and Nonparametric Analyses......Page 347
19.4 Multivariate Statistics, Classification, and Hypothesis Generation......Page 349
19.4.1 Ordination......Page 350
19.4.2 Cluster Analysis......Page 351
19.4.3 Phylogenetics and Parsimony Analyses......Page 352
19.4.4 Substantiating a Classification......Page 353
19.5 Modern Machine Learning Approaches......Page 354
19.6 Conclusions......Page 355
References......Page 356
SECTION III: Applied Chapters......Page 358
20.1 Introduction......Page 360
20.2.1 Vegetation Change and Microbial Communities......Page 361
20.2.2 Wildfire Effects on Microbial Communities......Page 363
20.2.3 Microbial Response to Permafrost Thaw......Page 364
20.3 Methodological Revolutions and New Frontiers......Page 366
References......Page 367
21.1 Introduction......Page 372
21.2 Assessment of Soil Infectious Potential and Soil Receptivity to Soilborne Diseases......Page 373
21.3 Different Types of Disease Suppressiveness......Page 375
21.4.1 Role of Biotic versus Abiotic Factors in Disease Suppression......Page 376
21.4.3 Identification of Organisms Involved in Disease Suppression......Page 377
21.4.4 Mechanisms Involved in Disease Suppression......Page 378
21.5.1 Early Studies and Importance of Diversity......Page 379
21.5.2 High-Throughput Meta-Omics Techniques in the Context of Disease Suppression......Page 380
21.6.1 Isolation and Selection of Biocontrol Agents......Page 383
21.6.3 Agricultural Practices Modulate Disease Suppressiveness......Page 384
References......Page 386
22.1.1.1 Rhizospheric versus Endophytic and Symbiotic Bacteria......Page 390
22.1.3.1 Nitrogen Fixation......Page 392
22.1.3.3 Iron Sequestration......Page 394
22.1.3.4 Synthesis of Phytohormones and/or Phytostimulators......Page 396
22.1.3.5 Increasing Plant Tolerance through ACC Deaminase Synthesis......Page 398
22.1.3.7 Antibiotics and Hydrogen Cyanide......Page 399
22.1.3.8 Cell Wall-Degrading Enzymes......Page 400
22.1.3.10 Bacteriophages......Page 401
22.1.3.11 Quorum sensing and Quenching......Page 402
22.2.2 Critical Factors Determining the Outcome of PGPB Applications......Page 404
22.3 Conclusions and Perspectives......Page 405
References......Page 406
23.1 Introduction......Page 410
23.2.1.1 Aliphatic and Alicyclic Compounds......Page 412
23.2.1.3 Hydrocarbon Biodegradation under Anaerobic Conditions......Page 413
23.3.1 Biodegradation of Chlorinated Aliphatic Compounds......Page 414
23.3.2 Biodegradation of Chlorinated Aromatic Compounds......Page 415
23.3.2.1 Chlorinated Benzenes and Phenols......Page 416
23.4 Biodegradation of Nitroaromatic Compounds......Page 417
23.5.1 Biodegradation of Pesticides......Page 418
23.5.2 Biodegradation of Pharmaceuticals......Page 420
23.5.3 Biodegradation of Plastics......Page 422
23.6.1 Activity-Based and Sequence-Based Metagenomics......Page 423
23.6.3 Expression of Degradative Genes in Soil......Page 424
23.7 Bioremediation......Page 425
23.7.1 Environmental Factors Affecting Bioremediation......Page 428
23.8 Concluding Remarks......Page 429
References......Page 430
Chapter 24 The Impact of Metal Contamination on Soil Microbial Community Dynamics......Page 432
24.2.1 Soil Metals and Concentrations......Page 433
24.2.1.1 Arsenic......Page 434
24.2.1.5 Lead......Page 435
24.3 Bioavailability......Page 436
24.5 Effects of Metals on Microbial Diversity......Page 437
24.6 Effects of Metals on Soil Microbial Biomass......Page 438
24.8.1.1 Extracellular Systems......Page 439
24.8.1.2 Outer Membrane Systems......Page 441
24.8.1.4 Cytoplasmic Membrane Systems......Page 442
24.8.1.5 Cytoplasmic Resistance Systems......Page 443
24.8.3 Genetic Adaptation......Page 444
24.8.4 Interactions between Metals and Antibiotics......Page 445
References......Page 446
25.1 Introduction......Page 450
25.2.1 Soil Management, Smart Farming, and the Microbiome......Page 451
25.2.2 The Microbiome in Agroecosystems and Its Modulation......Page 452
25.3.1 Cutting-Edge Plant/Soil Observation Methods and Deep Learning Robotics......Page 453
25.3.3 System-Level Soil Microbiome Modulation......Page 454
25.4.1 Land Use as a Modulator of Soil Microbiomes—Organic versus Conventional Agricultural Practices......Page 455
25.4.2 Modulation of Soil Microbiomes by Changes in Management......Page 456
25.6 Final Remarks and Outlook......Page 457
References......Page 458
Glossary......Page 460
Index......Page 488
