Modern Soil Microbiology, Third Edition

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 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 This timely reference/text integrates the principles of soil microbiology with novel insights into the physiology and activity of soil microbiota obtained by using the latest modern molecular analyses - investigating relationships between microbial communities, community structures, and function. Containing over 2950 references, tables, drawings, and photographs, this complete resource is an indispensable reference for soil and environmental microbiologists and biotechnologists, microbial ecologists, plant and soil virologists, plant pathologists, agronomists, soil scientists, agrobiologists, and researchers in phytopathology and geobiochemistry, and an excellent text for undergraduate and graduate students taking courses in soil microbiology