Soil Microbiology, Ecology and Biochemistry

5th Edition - August 30, 2023

Editors: Eldor Paul, Serita Frey

Hardback ISBN:

9 7 8 - 0 - 1 2 - 8 2 2 9 4 1 - 5

eBook ISBN:

9 7 8 - 0 - 1 2 - 8 2 3 4 1 5 - 0

Soil Microbiology, Ecology, and Biochemistry, Fifth Edition addresses the increasingly important field of soil biota and their interactions in research and education. Soil biota… Read more

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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.

Cover image
Title page
Table of Contents
Copyright
Contributors
Preface
Acknowledgment
Chapter 1. Continuing our excellence in soil microbiology, ecology, and biochemistry and using it to achieve a sustainable future
1.1. The scope and challenges
1.2. A brief history of our field
1.3. Putting it all together
Chapter 2. The habitat of the soil biota
2.1. Introduction
2.2. Soil formation
2.3. Nature of soil components
2.4. Pore space
2.5. Soil hotspots
2.6. Soil water
2.7. Soil aeration
2.8. Soil solution chemistry
2.9. Soil temperature
2.10. Environmental factors, temperature, and moisture interactions
Chapter 3. Soil bacteria and archaea
3.1. General introduction to bacteria and archaea
3.2. Metabolism and physiology
3.3. Microbial adaptations to the terrestrial environment
3.4. Major lineages of bacteria and archaea in soil
3.5. Phylogeny and function in the bacteria and archaea
3.6. Summary
3.7. Further reading and resources
Chapter 4. Fungi in soil: a rich community with diverse functions
4.1. Introduction
Supplemental material
Chapter 5. Soil fauna: occurrence, biodiversity, and roles in ecosystem function
5.1. Introduction
5.2. Overview of faunal biodiversity in soils
5.3. Protists: microbes among “fauna”
5.4. Microfauna
5.5. Mesofauna
5.6. Macrofauna
5.7. Roles of soil fauna in ecosystems and societal impacts
5.8. Summary
Chapter 6. Molecular and associated approaches for studying soil biota and their functioning
6.1. Introduction
6.2. Omics in the context of soil biota
6.3. Direct extraction, relic DNA, and cell separation for omic analyses
6.4. The use of biomarkers and metabarcoding for diversity studies
6.5. Meta-omics of soil biota: read-centric data analysis approaches
6.6. Meta-omics of soil biota: from potential to function
6.7. The new era of genome-resolved metagenomics
6.8. Big data challenges in molecular analyses of soil biota
6.9. Isotope-enabled molecular analyses of soil biota
6.10. From nanometer-scale cells to global-scale questions
Chapter 7. Physiological and biochemical methods for studying soil biota and their functions
7.1. Introduction
7.2. Scale of investigations and collection of samples
7.3. Storage and pretreatment of samples
7.4. Microbial biomass
7.5. Compound-specific analyses of microbial biomass and microbial community composition
7.6. Isotopic composition of microbial biomass and signal molecules
7.7. Physiological analyses
7.8. Enzyme activities
7.9. Imaging microbial activities
7.10. Functional diversity
7.11. Ecological approaches to understand and manipulate community composition
Chapter 8. The spatial distribution of soil biota and their functions
8.1. Introduction
8.2. The biogeography of soil biota and their functions
8.3. Vertical distributions within the soil profile
8.4. Microscale heterogeneity of soil organisms
8.5. Summary
Chapter 9. Biotic metabolism in soil
9.1. Introduction
9.2. Foundations of soil biotic metabolism
9.3. Metabolic classification of soil organisms
9.4. Cellular energy transformations
9.5. Examples of biotic metabolism in soil
9.6. Unifying views of biotic metabolism in soil
Chapter 10. The ecology of soil biota and their function
10.1. Introduction
10.2. Mechanisms that drive community structure
10.3. Consequences of microbial community structure for ecosystem function
10.4. Conclusion
Chapter 11. Plant–soil biota interactions
11.1. Soil biota: definitions and functions
11.2. The rhizosphere and its inhabitants
11.3. Mycorrhizal fungi
11.4. Threats to soil biota–plant interactions
11.5. Insights into plant–soil biota through -omics approaches
11.6. How soil microbiota improve plant responses to abiotic stress factors
11.7. Summary
Chapter 12. Soil carbon formation and persistence
12.1. Introduction
12.2. Short- and long-term C cycles
12.3. Soil organic carbon
12.4. Inputs for soil organic carbon formation
12.5. Developing a stabilization framework for soil organic carbon
12.6. Climate impacts on soil organic carbon persistence
12.7. Land use and management impacts on surface and subsurface soil organic carbon
12.8. Climate sensitive ecosystems and soil organic carbon persistence
12.9. Synthesis and outlook for soil organic carbon research
Chapter 13. Methods for studying soil organic matter: nature, dynamics, spatial accessibility, and interactions with minerals
13.1. Introduction
13.2. Quantifying soil organic matter
13.3. Fractionation methods
13.4. Characterization methods
13.5. Visualization methods
13.6. Methods to measure the turnover rate of soil organic matter
Chapter 14. Nitrogen transformations
14.1. Introduction
14.2. Nitrogen fixation
14.3. Nitrogen mineralization and immobilization
14.4. Nitrification
14.5. Denitrification
14.6. Other nitrogen transformations in soil
14.7. Nitrogen movement in the landscape
Chapter 15. Biological transformations of mineral nutrients in soils and their role in soil biogeochemistry
15.1. Introduction
15.2. Nutrient needs of soil biota
15.3. Effect of soil biota on inorganic nutrient transformations
15.4. Applied examples of interconnections between biotic community/activity and mineral nutrient transformations
Chapter 16. Advancing quantitative models of soil microbiology, ecology, and biochemistry
16.1. Introduction
16.2. Justification for modeling
16.3. Modeling approaches
16.4. Modeling across scales
16.5. Model-data integration
16.6. Recommendations to advance soil models
16.7. Conclusion
Chapter 17. The application of knowledge in soil microbiology, ecology, and biochemistry (SMEB) to the solution of today’s and future societal needs
17.1. Introduction
17.2. SMEB science and the frameworks for sustainable development
17.3. The grand challenge for global soils: food, energy, and water in a changing climate
17.4. Soil biota and earth system processes
17.5. The organization of SMEB science concepts and information
17.6. Anthropogenic impacts on the SMEB food web
17.7. Applications of SMEB science
17.8. Literacy, education, and engagement
17.9. Concluding remarks
Index