Mycoagroecology

Elizabeth “Izzie” Gall graduated from Tufts University in 2015 with a plant biology degree and a fierce passion for mycology. As an intern at the New York Botanical Garden, she founded Morel Dilemma, a podcast intended to impart her love of fungi to listeners of diverse backgrounds. After the internship ended, Izzie worked as a laboratory technician at New York University but continued the podcast, researching and producing episodes about mushroom cultivation, mycorrhizal relationships, foraging practices and safety, and fungi in the fossil record, among other topics. In 2017, Izzie attended graduate school in mycology and plant pathology at Michigan State University before returning to outreach. She is delighted to bring readers of all levels to a deeper understanding of fungi and their utility in natural and agricultural spaces. Izzie currently lives in Knoxville, Tennessee, U.S.A. with her husband Nate. Noureddine Benkeblia is a Professor of Crop Science, Department of Life Sciences, Faculty of Science and Technology, University of the West Indies Mona Campus, Jamaica. He is also Head of the Laboratory of Crop Science (Life Sciences Department) and Head of the Laboratory of Tree Fruits and Aromatic Crops (Biotechnology Centre), and coordinator of the graduate agriculture programmes. His main research areas focus on the environmental stresses on the physiology and biochemistry of crops including pre- and postharvest metabolism, and the metabolome. Prof. N. Benkeblia has an extensive research (more than 30 years) experience in horticultural sciences, and teaching at undergraduate, graduate and postgraduate levels in many countries. Prof. N. Benkeblia published over 230 publications including books, chapters and research papers. His is member of many international scientific societies NGO, and was recipient of many awards. He is also Associate Editor of several scientific journals e.g. Canadian Journal of Plant Science and PLOS Climate among others.

INTRODUCTION

1 Nutrient Cycling and Trophic Lifestyles (Elizabeth Gall and Noureddine Benkeblia)

1.1 Photosynthesis: Primary Calorie Production

1.2 Primary and Secondary Metabolites

1.3 The Carbon Cycle

1.4 The Nitrogen Cycle

1.5 Heterotroph Lifestyles

1.5.1 Ingestive Heterotrophs

1.5.2 Absorptive Heterotrophs

1.6 Agroecological Applications

2 Evolution and Symbiosis (Elizabeth Gall)

2.1 Fitness and Genes

2.2 Species

2.3 Evolution and Evolutionary Pressures

2.4 Coevolution and Symbiosis

2.4.1 Mutualism

2.4.2 Predators and Prey

2.4.3 Competition

2.4.4 Commensalism and Parasitism

2.5 Context Dependence of Symbiosis

2.6 Agroecological Applications

3 Population Dynamics (Elizabeth Gall)

3.1 Energy Flow in Ecosystems

3.2 Growth Curves

3.3 Carrying Capacity and Population Cycles

3.4 Agroecological Applications

4 The Kingdom Fungi (Steven Stephenson and Elizabeth Gall)

4.1 Basic Structures of Fungi

4.2 Basic Classification of Fungi and Fungus-Like Organisms

4.2.1 Slime Molds

4.3 Taxonomy of Macrofungi

4.4 Taxonomy of Microfungi

4.5 Sexual Reproduction

4.5.1 Basidiomycetes

4.5.2 Ascomycetes

4.6 Asexual and Sexual Stages

4.7 Fundamental Niches of Fungi

4.7.1 Saprotrophic Fungi

4.7.2 Fungi in Symbioses

4.8 Secondary Metabolites of Interest

4.8.1 Culinary Use

4.8.2 Poisons or Toxins

4.8.3 Medicinal Compounds

5 Limiting Factors in Agriculture (Noureddine Benkeblia)

5.1 Meteorological Limiting Factors

5.1.1 Extreme Temperature as a Limiting Factor

5.1.1.1 High Temperatures

5.1.1.2 Low Temperatures

5.1.1.3 Long-Term Effects of Extreme Temperatures

5.1.2 CO2 Concentration as a Limiting Factor

5.2 Where Meteorological and Land Factors Meet: Water as a Limiting Factor

5.3 Limiting Land Factors: Nutrient Supply

5.3.1 Nitrogen (N)

5.3.2 Phosphorus (P)

5.3.3 Potassium (K)

6 Principles of Crop Breeding and Productivity (Elizabeth Gall)

6.1 Artificial Evolutionary Pressure

6.2 Metabolite Limits of Selective Breeding

6.3 Photosynthetic Limits of Selective Breeding

6.4 Evolved Alternatives to C3 Photosynthesis

6.4.1 C4 Photosynthesis

6.4.2 CAM Photosynthesis

6.4.3 Evolutionary Limits

6.5 Other Methods to Increase Yields and Efficiency

6.5.1 Intercropping

6.5.2 Crop Rotation

6.5.3 Directed Genetic Modification

6.6 Developing Cooperative Varieties of Plants and Fungi

7 Pests and Pest Management Methods (Juan F. Barrera)

7.1 Humans Versus Pests

7.2 Pest Management Strategies and Tactics

7.3 Economics and Ecology of Pests

7.3.1 The Economic Approach

7.3.2 The Ecological Approach

7.3.2.1 r-Pests

7.3.2.2 K-Pests

7.3.2.3 Intermediate Pests

7.4 The Future of Pest Management

7.4.1 Biologically Intensive IPM

7.4.2 Agroecologically Integrated Pest Management

7.4.3 Ecologically Based Pest Management (EBPM)

7.4.4 Total System Approach

7.4.5 Integrated Management of Biodiversity (IMB)

7.4.6 Integrated Crop Management (ICM)

7.4.7 Integrated Production

7.4.8 Integrated Agroecosystem Design and Management (IADM)

7.4.9 Crop Health and Salutogenesis

7.4.10 Holistic Pest Management (HPM)

7.5 Conclusion

8 Economic Factors in Agriculture (Elizabeth Gall and Barbara Laff)

8.1 Supply and Demand

8.1.1 Agricultural Supply: Balancing Inputs and Outputs with Costs and Income

8.1.2 Agricultural Demand: Glut Price Cycles

8.2 Farm Sizes and Types

8.2.1 Farm Consolidation

8.3 Market Distortions

8.3.1 Government Interventions

8.4 Other Factors

8.4.1 Ecological Considerations

8.4.2 Intellectual Property Law

8.4.2.1 Plants as Intellectual Property

8.4.2.2 Patents and Seed Re-Use

8.5 Conclusion

9 The Green Revolution: Agricultural Shifts of the 20th Century (Elizabeth Gall)

9.1 The United States: From Dust Bowl to Green Revolution

9.2 Mexico and The Initial Green Revolution

9.3 The Philippines, China, and Southeast Asia: Global Attention and Wild Success

9.4 Patterns of the Green Revolution

9.5 Environmental Impacts of High-Input Systems

9.5.1 Fertilizer

9.5.2 Irrigation

9.5.3 Monoculture

9.6 Economic Impact

9.7 Government Interventions

9.8 Conclusion

MYCOAGROECOLOGY

10 The Second Green Revolution and the Role of Mycoagroecology (Elizabeth Gall)

10.1 Mycology: Revealing the Fungal Roles of Partners, Pests, Pest-Control Agents, and Products

10.2 Agroecology: Integrating Productivity and Sustainability

10.2.1 Industrial Farms Value Production over Ecosystem Balance

10.2.2 Buffering the Ecosystem from the Farm

10.2.3 Closing the Loop: The Farm as an Island Ecosystem

10.2.4 The Farm as a Productive Portion of the Ecosystem

10.2.5 Incorporating Other Techniques

10.3 Mycoagroecology

10.3.1 Partners

10.3.2 Pests and Pest-Control Agents

10.3.3 Products

10.4 Mycoagroecology is Compatible with the Goals of the Second Green Revolution

10.4.1 Address “Orphan” Regions and Crops

10.4.2 Return to Polyculture

10.4.3 Reduce the Need for Synthetic Inputs

10.4.4 Maintain Smallholder Competitiveness

10.5 Conclusion

FUNGI AS PARTNERS

11 Plant-Fungal Mutualisms (Jason C. Slot)

11.1 Plant-Fungal Mutualisms Vary According to Plant "Compartments"

11.2 Arbuscular Mycorrhizal Fungi Colonize Diverse Plant Roots Worldwide

11.3 Ectomycorrhizal Fungi Colonize Roots of Woody Plants in Northern and Temperate Forests

11.4 Mycorrhizal Relationships are Structurally and Ecologically Diverse

11.4.1 Plants in a Community Can Benefit from Shared Mycorrhizal Networks

11.4.2 Mycoheterotrophs Exploit Plant-Fungal Mutualisms

11.5 Endophytic Fungi are Common Residents of Plant Tissues

11.6 Fungi can Provide Benefits to Other Plant Mutualisms

11.7 Plant-Fungal Mutualisms Require an Adapted Fungal Community

12 Incorporating Microbes into Agricultural Soils (Elizabeth Gall)

12.1 Types of Soil Microbes

12.1.1 Arbuscular Mycorrhizal (AM) Fungi

12.1.2 Ectomycorrhizal (ECM) Fungi

12.1.3 Root Endophytes

12.1.4 Other Soil Microbes

12.2 Industrial Agricultural Practices Destroy Soil Microbial Communities

12.2.1 Monoculture

12.2.2 Other Microbiome-Damaging Practices

12.3 Restoring Microbial Populations is Possible and Effective

12.4 Methods for Reintroducing Microbes to Agricultural Soils

12.4.1 Soil Inoculation

12.4.2 Trap Plants

12.4.3 Seed Coating

12.4.4 Monospecies vs. Community Inoculation

12.5 Management Practices for Soil Microbe Retention

12.6 Conclusion

FUNGI AS PESTS AND PEST-CONTROL AGENTS

13 Fungal Diseases in Agriculture: Significance, Management, and Control (Noureddine Benkeblia)

13.1 Significance of Fungal Diseases in Agriculture

13.2 Management and Control of Fungal Diseases in Agriculture

13.2.1 Chemical Control

13.2.2 Cultural Methods and Integrated Pest Management (IPM)

13.2.3 Biological Control Agents (BCA)

14 Fungal Pathogens in Forested Ecosystems (Denita Hadziabdic, Aaron Onufrak, and Romina Gazis)

14.1 Detection Tools and Surveillance Methods

14.2 Fusarium Dieback – Invasive Shot Hole Borers

14.2.1 Disease Biology and Impact

14.2.2 Detection and Identification of the Pathogen and Vector

14.3 Laurel Wilt

14.3.1 Disease Biology and Impact

14.3.2 Detection and Identification of the Pathogen and Vector

14.4 Thousand Cankers Disease

14.4.1 Disease Biology and Impact

14.4.2 Detection and Identification of the Pathogen and Vector

14.5 Management of Fungal Diseases in Forested Areas

14.5.1 Cultural Practices

14.5.1.1 Quarantine and Sanitation

14.5.1.2 Resource Management

14.5.1.3 Plant Breeding

14.5.2 Chemical Management

14.5.3 Biological Control

15 Fungal Interactions with Other Pests (Guillermo Valero-David and Jason C. Slot)

15.1 Insects

15.1.1 Fungi are an Important Food Source for Insects and Their Relatives

15.1.1.1 Attine Ants

15.1.1.2 Macroterminiti Termites

15.1.1.3 Ambrosia Beetles

15.1.2 Insects are Important Vectors of Plant Pathogenic Fungi

15.1.3 Fungi are Important Pathogens of Insects

15.1.3.1 Entomopathogenic Fungi in Soils

15.1.4 Fungal-Insect Interactions are Important Factors in Ecosystem Processes

15.2 Nematodes

15.2.1 Nematodes Consume Fungi, Resulting in Varied Impacts on Agroecosystems

15.2.2 Diverse Fungi Attack and Consume Nematodes

15.2.3 Nematodes and Plant Pathogenic Fungi Can Act Synergistically to Cause Plant Disease

15.2.4 Coevolution of Fungi and Nematodes Has Resulted in Diverse Associations

FUNGI AS PRODUCTS

16 Principles of Modern Fungal Cultivation (Elizabeth Gall)

16.1 Protein Value of Mushrooms

16.2 Limiting Factors in Mushroom Cultivation

16.2.1 Carbon Dioxide Concentrations

16.2.2 Carbon and Nitrogen

16.2.3 Other Macronutrients

16.2.4 Water

16.2.5 Light

16.2.6 Micronutrients

16.3 Modern Mushroom Cultivation

16.3.1 Starting Substrate

16.3.2 Mushroom Spawn

16.4 Genetic Aspects of Mushroom Cultivation

17 Integrating Fungi into Existing Farms (Elizabeth Gall)

17.1 Mushroom Cultivation Recycles Agro-Industrial Waste

17.2 Abundance of Lignocellulosic Waste

17.3 Selecting Substrates and Fungal Strains

17.4 Mushroom Cultivation Locations

17.4.1 Mushroom Cultivation in Buildings

17.4.2 Mushroom Cultivation in Woods

17.4.3 Mushroom Cultivation in Fields

17.4.4 Co-Cropping with Ectomycorrhizal Fungi

17.5 Other Potential Uses of Mushrooms

17.5.1 Mushroom Growing Kits

17.5.2 Spent Mushroom Substrate

17.5.3 Mycoremediation of Damaged Landscapes

17.5.4 Bioprospecting: “Pests” with Agricultural Utility

17.6 Conclusion

18 Fungi in Food Processing (Noureddine Benkeblia)

18.1 Fermented and Aged Food Products

18.1.1 Fermented Foods are Diverse and Numerous

18.1.2 Breads

18.1.3 Fermented Meats

18.1.4 Cheeses

18.1.5 Yogurts and Other Fermented Dairy Products

18.2 Fermented Beverages

18.2.1 Alcoholic Fruit-Based Beverages (Wines)

18.2.2 Alcoholic Grain-based Beverages (Beers)

18.2.3 Other Alcoholic Beverages

18.2.4 Non-Alcoholic Fermented Beverages

18.3 Food Additives and Ingredients

18.4 Bioprocessing and Novel Food Production by Fungi