Assessing the Microbiological Health of Ecosystems

Cover
Title Page
Copyright Page
Dedication Page
Contents
List of Contributors
Preface
Chapter 1 Ecosystems Function Like Interlocking Puzzles: Visually Interpreting the Concept of Niche Space Plus a Brief Tour Through Genetic Hyperspace
	1.1 Introduction
	1.2 Three People Who Historically Defined the Concept of an Ecological Niche
		1.2.1 Joseph Grinnell’s 1917 Description of an Ecological Niche
		1.2.2 Charles Elton’s 1927 Description of an Ecological Niche
		1.2.3 Evelyn Hutchinson’s 1957 Description of an Ecological Niche
	1.3 How Does a Species Become Established in a Niche?
	1.4 Relationship Between the Requirements of Niche and Habitat
		1.4.1 Defining a Species Habitat Requirements and Inclusion of the Physiological Boundaries Concept
		1.4.2 Hutchinson’s Description and Depiction of Niche Space
	1.5 Using Visual Analogies to Represent the Concept of a Species Niche as Being a Multidimensional Space Which has Complex Surface Geometry
		1.5.1 A Broader Consideration of the Variables that Would Define Niche Space
		1.5.2 Imagining that Interactions Between Species Occur at the Surfaces of Their Niche Spaces
		1.5.3 Three Mammal Species as Examples of Niche Space Interactions: The Koala, the Mexican Collared Anteater, and the Northern Atlantic Right Whale
		1.5.4 One Insect Species as an Example of Niche Space Interactions, the Raspberry Aphid
	1.6 Competition for the Control of Niche Space
		1.6.1 Opportunities, Intrusions and Challenges Result in the Control of Niche Space
		1.6.2 Using Visual Analogies for There Being Different Ways to Occupy the Same Total Volume of Niche Space
	1.7 Defining the Concept of Genetic Hyperspace
		1.7.1 Using Visual Analogies to Help Understand the Concept of Genetic Hyperspace
		1.7.2 Examples of Organisms Whose Symbioses Represent Interlocking Niche Spaces and Parallel or Common Genetic Trajectories
		1.7.3 Relating the Concept of Genetic Trajectories and the Host Specificity of Viruses
	1.8 Conclusions
	Acknowledgements
	References
Chapter 2 Human and Climatic Drivers of Harmful Cyanobacterial Blooms (CyanoHABs)
	2.1 What are CyanoHABs?
	2.2 Human and Climatic Drivers of CyanoHABs
	2.3 Nutrient Management
		2.3.1 Phosphorus Management
		2.3.2 Nitrogen Management
	2.4 Climatic Drivers
	2.5 The Ultimate Challenge of the Twenty-First Century: Controlling HABs Against a Backdrop of Changing Climatic Conditions
	2.6 Summary
	Acknowledgements
	References
Chapter 3 Biodegradation of Environmental Pollutants by Autochthonous Microorganisms – A Precious Service for the Restoration of Impacted Ecosystems
	3.1 Introduction
	3.2 Environmental Pollutants of Major Concern
		3.2.1 Pharmaceuticals
		3.2.2 Pesticides
		3.2.3 Petroleum Hydrocarbons
	3.3 Current Remediation Technologies Targeting Pharmaceuticals, Pesticides, and Petroleum Hydrocarbons
	3.4 Role of Environmental Microorganisms on the Removal of Pharmaceuticals, Pesticides, and Petroleum Hydrocarbons
	3.5 Filling in the Gaps – Autochthonous Microorganisms as Tools for the Bioremediation of Environmental Pollutants
	3.6 Final Considerations
	3.7 Acknowledgments
	References
Chapter 4 Early Biofilm Accumulation in Freshwater Environments on Different Types of Plastic
	4.1 Introduction
		4.1.1 The Importance of Freshwater Study
		4.1.2 Plastics in Fresh Water, or How a Solid Becomes Part of a Liquid
		4.1.3 Additional Materials Found Associated with the Plastic
		4.1.4 Can Plastics Be Removed from Freshwater and Wastewater?
		4.1.5 The Great Lakes, Their Importance, and Their Interactions with Plastics
		4.1.6 Early Events: Importance, Criticality, and Need for Study
	4.2 Background
		4.2.1 Typical and Historical Ways this Field has been Researched
	4.3 Results
		4.3.1 Research Methodology
		4.3.2 A Census and Diversity
	4.4 Discussion
		4.4.1 Possible Causes for Population Dynamics Over Time
	4.5 Summary
		4.5.1 General Conclusions
		4.5.2 Further Research
	References
Chapter 5 Identification of Sentinel Microbial Communities in Cold Environments
	5.1 Introduction
	5.2 Microorganisms as Sentinels of Global Warming
	5.3 Microorganisms as Sentinels of Contamination
	5.4 How Biogeochemical Cycles Can Change
		5.4.1 The Carbon Cycle
		5.4.2 The Nitrogen Cycle
		5.4.3 The Iron Cycle
		5.4.4 The Phosphorus Cycle
		5.4.5 The Silica Cycle
		5.4.6 The Sulfur Cycle
	5.5 Causes of Alterations in Microbial Communities
		5.5.1 Global Warming
		5.5.2 Introduction of Nonindigenous Species
	5.6 Human Activities That Can Be Influenced by Microbial Communities Alterations
	5.7 Methods and Techniques to Identify Sentinel Microorganisms
		5.7.1 Chemical Analysis of Glacier Ice, Meltwater, and Runoff Waters
		5.7.2 Identification of Sentinel Microbial Communities
		5.7.3 Relationship Between the Chemical Composition and Microbial Communities
	5.8 Conclusion
	Acknowledgments
	References
Chapter 6 Analyzing Microbial Core Communities, Rare Species, and Interspecies Interactions Can Help Identify Core Microbial Functions in Anaerobic Degradation
	6.1 Introduction
		6.1.1 Anaerobic Degradation Technology – Its Multiple Benefits and Unlocked Potential
		6.1.2 Microbiology in the Anaerobic Degradation Process
	6.2 Defining Key Microorganisms and Core Communities in Anaerobic Degradation Systems
		6.2.1 Approaches Used to Identify Core Communities
	6.3 Core Definitions Applied to Anaerobic Digester Microbial Communities
		6.3.1 Interpretation of Results and the Importance of Consistent Use of Phylogenetic Level
		6.3.2 Impacts of Deterministic and Stochastic Factors and of Temporal Dynamics on Core Communities
	6.4 Rare Species, Diversity Indices, and Links to Presence of Core Communities
		6.4.1 Rare Species and Their Importance to Community Functioning
	6.5 Network Analysis
		6.5.1 Definition and Construction
		6.5.2 Link with Core Community
		6.5.3 Identifying Keystone Species Using Network Analysis
	6.6 Defining Core Microbiota for Functionality
		6.6.1 Using 16S rRNA Gene Data to Estimate Functions
		6.6.2 Using Whole-Genome Sequencing to Estimate Functions
	6.7 Concluding Remarks and Future Prospects
	References
Chapter 7 Role of Microbial Communities in Methane and Nitrous Oxide Fluxes and the Impact of Soil Management
	7.1 Introduction
		7.1.1 The Cycling of Carbon and Nitrogen in Terrestrial Ecosystems
		7.1.2 The Importance of Methane and Nitrous Oxide Fluxes in Climate Change Scenarios
	7.2 The Role of Microorganisms in Methane and Nitrous Oxide Fluxes
		7.2.1 Methane
		7.2.2 Nitrous Oxide
	7.3 Methane and Nitrous Oxide Emission Mitigation Strategies
		7.3.1 Rice Cultivation
		7.3.2 Mineral Fertilization
		7.3.3 Organic Fertilization and Livestock Chain
		7.3.4 Biochar Amendment and Liming
	7.4 Summary and Conclusions
	References
Chapter 8 Impact of Microbial Symbionts on Fungus-Farming Termites and Their Derived Ecosystem Functions
	8.1 Introduction
		8.1.1 Ecosystem Services Provided by Insects
		8.1.2 The Evolution of Microbial Symbioses in the Blattodea
		8.1.3 The Role of Microbial Symbioses in Fungus-Farming Termite Ecosystem Services
	8.2 Ancient Association of Co-Diversifying Symbiont Community
		8.2.1 Termite and Termitomyces Evolution, Diversification, and Symbiont Roles
		8.2.2 Bacterial Communities
		8.2.3 Additional Microbial Symbionts
	8.3 Microbial Contributions to Nutrient Cycling
		8.3.1 The Plant Biomass Decomposition Process
		8.3.2 Enzymatic Contributions from Termitomyces and Bacteria
		8.3.3 Oxidative Enzymes and Nonenzymatic Plant Biomass Decomposition by Termitomyces
	8.4 Microbial Contributions to Colony Health
		8.4.1 Termitomyces Role
		8.4.2 Bacterial Roles
	8.5 How Termite Activity and Microbial Processes Affect the Ecosystems Within Which They Reside
		8.5.1 Impacts of Live Colony Activity
		8.5.2 Impacts When Colonies Die
	8.6 Interactions with and Impacts on Humans
		8.6.1 Importance as Agricultural Pests
		8.6.2 Soil for Building Material and Inspiration for Biomimicry
		8.6.3 Termitomyces Bio-Economies for Food and Medicine
	8.7 Conclusions
	Acknowledgments
	References
Chapter 9 The Ecosystem Role of Viruses Affecting Eukaryotes
	9.1 Introduction
		9.1.1 Eukaryogenesis
		9.1.2 Infectious Transmission of a Virus
		9.1.3 Transfer of Genes from Virus to Host and Endogenous Transmission of a Virus
		9.1.4 Genes Also May Be Transferred in the Other Direction, from Host to Virus
		9.1.5 An Introduction to the Hosts Antiviral Response Mechanisms
		9.1.6 Understanding Niches and the Species Which Occupy Them
		9.1.7 Coevolution of Virus and Host Constantly Redefines Their Respective Niches
	9.2 Three Historically Important Discoveries Regarding the Viruses that Affect Eukaryotes
		9.2.1 Tobacco Mosaic Virus (Crimea, 1890)
		9.2.2 Influenza Virus (United States, 1918)
		9.2.3 Coronavirus (China, 2019)
	9.3 The Chalk Cliffs of Dover Represent an Ecosystem Impact Associated with Viruses of Phytoplankton
	9.4 Examples of Viral Induced Phenotypic Changes in Fungal Hosts
		9.4.1 Viral Induced Hypervirulence
		9.4.2 Viral Induced Hypovirulence
		9.4.3 Viral Induced Thermotolerance
	9.5 Ecological Interactions Between Viruses and Insects
		9.5.1 Viral Induced Phenotypic Changes in Honeybees
		9.5.2 Polyhedrosis Viruses are a Natural Mechanism for Biological Control of Lepidopteran Larvae
		9.5.3 Interactive Ecology of Aphids, Their Predators, and Viruses
		9.5.4 Endogenous Viruses that Enable the Replication of Parasitoid Wasps
		9.5.5 Using Parasitic Bacteria to Prevent Mosquito Vectoring of Viruses
	9.6 Endogenous Viruses Enable Placentation in Vertebrates
		9.6.1 Placental Mammals
		9.6.2 Placental Reptiles
	9.7 Summary
	Acknowledgments
	References
Index
EULA