Fundamentals of Soil Ecology

Fundamentals of Soil Ecology
Copyright
Preface
1 Introduction to Soil: Historical Overview, Soil Science Basics, and the Fitness of the Soil Environment
	1.1 Why Soil Ecology?
	1.2 The Historical Background of Soil Ecology
	1.3 Water as a Constituent of Soil
	1.4 Elemental Constitution of Soil
	1.5 How Soils Are Formed
	1.6 Profile Development
	1.7 Soil Texture
	1.8 Clay Mineral Structure
	1.9 Soil Structure
	1.10 Soils as Suppliers of Ecosystem Services
	1.11 Summary
2 Primary Production Processes in Soils: Roots and Rhizosphere Associates
	2.1 Introduction
	2.2 The Primary Production Process
		2.2.1 Zones of Root Growth and Activity
	2.3 Methods of Sampling
		2.3.1 Destructive Techniques
			2.3.1.1 The Harvest Method
			2.3.1.2 Isotope-Dilution Method
			2.3.1.3 Root-Ingrowth Technique
			2.3.1.4 Nondestructive Techniques
	2.4 Additional Sources of Primary Production
	2.5 Symbiotic Associates of Roots
	2.6 Mycorrhizal Structure and Function
		2.6.1 Commonalities between Rhizobia and Mycorrhiza for Colonizing Roots
	2.7 Ecosystem-Level Consequences of Ectomycorrhizal Function
	2.8 Actinorhiza
	2.9 Carbon Allocation in the Root/Rhizosphere
	2.10 Future Directions for Research on Roots and Mycorrhizal Function and Biodiversity
	2.11 Summary
3 Secondary Production: Activities of Heterotrophic Organisms—Microbes
	3.1 Introduction
	3.2 Compounds Being Decomposed
	3.3 Microbial Activities in Relation to Catabolism in Soil Systems
	3.4 Roles of Soil Protists in Soils
	3.5 Stocks of Carbon in Deep Soil, Faunal Influences
	3.6 Microbial Heterogeneity and Spatial Patterns in Soils
	3.7 Approaches for Estimating Microbial Numbers and Turnover
	3.8 Techniques for Measuring Microbial Communities
		3.8.1 Direct Measures of Numbers and Biomass
		3.8.2 Indirect Measures of Biomass: Chemical Methods
			3.8.2.1 The Chloroform Fumigation and Incubation Technique
			3.8.2.2 Chloroform Fumigation-Extraction Procedure
			3.8.2.3 Physiological Methods
			3.8.2.4 Additional Physiological Methods of Measuring Microbial Activity
			3.8.2.5 Enzyme Assays and Measures of Biological Activities in Soils
			3.8.2.6 Direct Methods of Determining Biological Activity
	3.9 Soil Sterilization and Partial Sterilization Techniques
	3.10 Conceptual Models of Microbes in Soil Systems
		3.10.1 Root-Rhizosphere Microbe Models and Experiments
		3.10.2 Soil Aggregation Models
		3.10.3 Models: Organism- and Process-Oriented
	3.11 Summary
4 Secondary Production: Activities of Heterotrophic Organisms—The Soil Fauna
	4.1 Introduction
	4.2 The Microfauna
		4.2.1 Distribution of Protozoa in Soil Profiles
		4.2.2 Impacts of Protozoa on Ecosystem Function
	4.3 The Mesofauna
		4.3.1 Rotifera
			4.3.1.1 Features of Body Plans and General Ecology
		4.3.2 Nematoda
			4.3.2.1 Nematode Feeding Habits
			4.3.2.2 Nematode Zones of Activity in Soil
			4.3.2.3 Nematode Extraction Techniques
		4.3.3 Tardigrada
		4.3.4 Microarthropods
			4.3.4.1 Collembola
				Families of Collembola
				Population Growth and Reproduction
				Collembolan Feeding Habits
				Collembolan Impacts on Soil Ecosystems
		4.3.5 Acari (Mites)
			4.3.5.1 Oribatid Mites
				Abundance and Diversity of Oribatid Mites
				Population Growth
				Oribatid Feeding Habits
				Oribatid Impacts on Soil Ecosystems
			4.3.5.2 Prostigmatic Mites
			4.3.5.3 Mesostigmatic Mites
			4.3.5.4 Astigmatine Mites
		4.3.6 Other Microarthropods
			4.3.6.1 Protura
			4.3.6.2 Diplura
			4.3.6.3 Microcoryphia
			4.3.6.4 Pseudoscorpionida
			4.3.6.5 Symphyla
			4.3.6.6 Pauropoda
		4.3.7 Enchytraeidae
	4.4 The Macrofauna
		4.4.1 Macroarthropods
			4.4.1.1 Importance of the Macroarthopods
			4.4.1.2 Isopoda
			4.4.1.3 Diplopoda
			4.4.1.4 Chilopoda
			4.4.1.5 Scorpionida
			4.4.1.6 Araneae
				Opiliones
				Solifugae
				Uropygi
			4.4.1.7 The Pteyrgote Insects
				Coleoptera
				Hymenoptera
				Diptera
				Isoptera
			4.4.1.8 Other Pterygota
			Gastropoda
				Sampling Techniques for Gastropods
		4.4.2 Oligochaeta—Earthworms
			4.4.2.1 Earthworm Distributions and Abundance
			4.4.2.2 Biology and Ecology
			4.4.2.3 Influence of Earthworms on Soil Processes
			4.4.2.4 Earthworm Management
			4.4.2.5 Earthworm Sampling and Identification
	4.5 General Attributes of Fauna in Soil Systems
	4.6 Faunal Feedbacks on Microbial Community Composition and Diversity
	4.7 Summary
5 Decomposition and Nutrient Cycling
	5.1 Introduction
	5.2 Integrating Variables
	5.3 Resource Quality, Climate, and Litter Breakdown
	5.4 Dynamics of Litter Breakdown
	5.5 Direct Measurement of Litter Breakdown
	5.6 Patterns of Mass Loss During Decomposition
	5.7 Effects of Fauna on Litter Breakdown Rates
	5.8 Nutrient Movement During Decomposition
	5.9 Nutrient Cycling Links in Soil Systems
	5.10 Role of Soil Fauna in Organic Matter Dynamics and Nutrient Turnover
	5.11 Global Change Experiments, Soil Fauna Effects on Decomposition
	5.12 Principal Characteristics of Soil Systems Governing SOM Dynamics
	5.13 Major Syntheses of Integrative Plant and Soil Functions
	5.14 Faunal Impacts in Applied Ecology—Agroecosystems
	5.15 Applied Ecology in Forested Ecosystems
	5.16 Summary
6 Soil Food Webs: Detritivory and Microbivory in Soils
	6.1 Introduction
	6.2 Physiological Ecology of Soil Organisms
	6.3 Energy Available for Detrital Food Chains and Webs
		6.3.1 Arenas of Interest
	6.4 A Hierarchical Approach to Organisms in Soils
	6.5 Future Research Prospects
	6.6 Summary
7 Soil Biodiversity and Linkages to Soil Processes
	7.1 Introduction
	7.2 Biodiversity in Soils and Its Impacts on Terrestrial Ecosystem Function
	7.3 Heterogeneity of Carbon Substrates and Effects on Soil Biodiversity
	7.4 Impacts of Species Richness on Ecosystem Function
	7.5 Models, Microcosms, and Soil Biodiversity
	7.6 Experimental Additions and Deletions in Soil Biodiversity Studies
	7.7 Problems of Concern in Soil Biodiversity Studies
	7.8 Why Is Soil Diversity So High?
	7.9 Biogeographical Trends in Diversity of Soil Organisms
8 Future Developments in Soil Ecology
	8.1 Introduction
	8.2 Roles of Soils in Carbon Sequestration
	8.3 Roles of Soils in the Global Carbon Cycle
	8.4 Problems in Modeling Soil Carbon Dynamics
	8.5 Biological Interactions in Soils and Global Change
		8.5.1 Changes in Soil Biodiversity in Relation to Global Climate Change
	8.6 Ecology of Invasive Species in Soil Systems: An Increasing Problem in Soil Ecology
	8.7 Soils and “Gaia”: Possible Mechanisms for Evolution of “the Fitness of the Soil Environment?”
	8.8 Importance of Natural History Collections to Informing Global Change Studies in the Future
	8.9 Soil Ecology in the Third Millennium
9 Laboratory and Field Exercises in Soil Ecology
	9.1 Introduction
	9.2 Root-Related Exercises
		9.2.1 Construction of a Simple Root Observatory (i.e., a Rhizotron)
		9.2.2 Minirhizotron Studies
		9.2.3 Sequential Sampling of Root Cores
		9.2.4 Root In-Growth Cores
	9.3 Process-Related Exercises
		9.3.1 Soil Respiration Studies
		9.3.2 Litter Decomposition Studies
	9.4 Soil Microbe and Protozoan Exercises
		9.4.1 Quantifying Mycorrhizal Fungi Colonization of Roots
		9.4.2 Analyses for Soil Microbial Biomass
			9.4.2.1 The Chloroform-Fumigation–K2SO4-Extraction Method
		9.4.3 Field Exercise for Soil Protozoan Activity and Biodiversity
	9.5 Soil Fauna Exercises
		9.5.1 Sampling and Enumeration of Nematodes
			9.5.1.1 Nematode Extraction: Baermann Funnel Method
			9.5.1.2 Killing and Fixing Nematodes With Hot and Cold Formalin (5%) (Precautionary Note: Conduct This Work in a Fume Hood)
		9.5.2 Sampling and Enumeration of Microarthropods
			9.5.2.1 Methods for the Study of Microarthropods
		9.5.3 Sampling and Enumeration of Macroarthropods
		9.5.4 Sampling and Enumeration of Enchytraeids
			9.5.4.1 Collection of Enchytraeids
			9.5.4.2 Sampling and Enumeration of Earthworms
			9.5.4.3 Sampling Exercise for Macroinvertebrates (Earthworms and Macroarthropods)
References
Index