
Microbial Life of Cave Systems
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The earth's subsurface contains abundant and active microbial biomass, living in water, occupying pore space, and colonizing mineral and rock surfaces. Caves are one type of subsurface habitat, being natural, solutionally- or collapse-enlarged openings in rock. Within the past 30 years, there has been an increase in the number of microbiology studies from cave environments to understand cave ecology, cave geology, and even the origins of life. By emphasizing the microbial life of caves, and the ecological processes and geological consequences attributed to microbes, this book provides the first authoritative and comprehensive account of the microbial life of caves for students, professionals, and general readers.
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Content
- Intro
- Contents
- Preface
- Contributing authors
- 1. Bringing Microbes into Focus for Speleology: An Introduction
- 1.1 Introduction
- 1.2 Energy to Sustain Subsurface Ecosystems
- 1.3 Historical Framework of Cave Microbiology Research and Collaboration
- 1.3.1 Research following the advent of molecular genetics techniques
- 1.3.2 Sulfidic cave research
- 1.3.3 Other cave research - nonsulfidic cave systems
- 1.4 The Future of Cave Microbiology Research
- 2. Methods for Characterizing Microbial Communities in Caves and Karst: A Review
- 2.1 Introduction
- 2.2 Culture-based Analyses
- 2.3 Culture-independent Analyses Based on rRNA Genes
- 2.3.1 rRNA gene (rDNA) cloning
- 2.3.2 High-throughput rRNA amplicon sequencing
- 2.3.3 Terminal restriction fragment length polymorphism (T-RFLP)
- 2.3.4 Denaturing gradient gel electrophoresis (DGGE)
- 2.3.5 Fluorescence in situ hybridization (FISH)
- 2.4 PCR-Based Functional Gene Analysis
- 2.5 Other Methods
- 2.6 Metagenomics
- 2.7 RNA-Based Analyses and Other "-Omics" Approaches
- 2.8 Case Study: Sulfidic Cave Snottites
- 2.9 Conclusions
- 3. "A Grand, Gloomy, and Peculiar Place": Microbiology in the Mammoth Cave Region
- 3.1 Introduction to Mammoth Cave and the Region
- 3.1.1 The Mammoth Cave region
- 3.1.2 Mammoth Cave National Park
- 3.2 Microorganisms in Caves
- 3.2.1 Bacteria and Archaea
- 3.2.2 Early microbiological studies from Mammoth Cave
- 3.2.3 Recent microbiological studies from Mammoth Cave
- 3.2.4 Actinobacteria
- 3.3 Cave Ecosystem Energy
- 3.3.1 Detrital-based ecosystems
- 3.3.2 Phototrophy due to tourism
- 3.3.3 Chemolithoautotrophically based cave ecosystems
- 3.4 Geomicrobiology
- 3.4.1 Saltpeter formation
- 3.4.2 Ferromanganese deposits
- 3.5 Eukaryotic Microorganisms
- 3.5.1 Protozoa and algae
- 3.5.2 Fungi
- 3.6 Infections and Parasites
- 3.6.1 Tuberculosis
- 3.6.2 Parasites
- 3.7 Human Impact
- 3.8 Microbes and Cave Crickets
- 3.8.1 Cricket crop microbes
- 3.8.2 Crickets and fungi
- 3.8.3 Cricket parasites
- 3.9 Conservation of Microbes
- 3.10 Conclusions
- 4. Starving Artists: Bacterial Oligotrophic Heterotrophy in Caves
- 4.1 Introduction
- 4.1.1 Oligotrophy
- 4.2 To Grow or Not to Grow
- 4.3 The Culture-independent View of Heterotrophy in Caves
- 4.4 Diversity of Oligotrophic Microbes in Caves
- 4.4.1 Old friends: The Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes
- 4.4.2 ... and new: The Planctomycetes, Chloroflexi, Acidobacteria, and Verrucomicrobia
- 4.5 Something Wicked This Way Comes - Understanding Carbon in Caves
- 4.6 Whether 'Tis Nobler to Grow
- 4.7 Out, Out, Brief Candle - Competition and Death in Cave Oligotrophs
- 4.8 Heterotrophic Community Dynamics in Caves - If You Can Look into the Seeds of Time and Say Which Grain Will Grow and Which Will Not
- 5. Bacterial and Archaeal Diversity on Cave Speleothem and Rock Surfaces: A Carbonate Cave Case Study from Kartchner Caverns
- 5.1 Introduction
- 5.2 Bacterial and Archaeal Diversity on Caves Surfaces
- 5.3 Microbial Energy Dynamics in Caves
- 5.4 Kartchner Caverns: An Epigenic Limestone Cave Case Study
- 5.4.1 Speleothem community diversity analysis
- 5.4.2 Cave functional dynamics - a metagenomic approach
- 5.4.3 The importance of culture-based characterizations
- 5.5 Conclusions
- 6. Microbial Slime Curtain Communities of the Nullarbor Caves
- 6.1 Introduction
- 6.1.1 The Nullarbor Cave environment
- 6.2 Microbial Slime Curtains
- 6.2.1 Microscopy and association of calcite crystals
- 6.3 Community Membership
- 6.4 Metabolism of Microbial Slime Communities
- 6.4.1 Weebubbie Cave nitrogen and carbon cycling
- 6.5 Comparison of Metabolic Profiles from Other Habitats
- 6.6 Conclusions
- 7. Microbial Diversity and Manganese Cycling: A Review of Manganese-oxidizing Microbial Cave Communities
- 7.1 Introduction
- 7.2 Manganese Oxides in Caves
- 7.3 Functions and Mechanisms of Manganese Oxidation
- 7.3.1 Enzymes associated with manganese oxidation
- 7.3.2 Mangenese-oxidizing bacteria and fungi
- 7.3.3 Mechanisms of microbialmanganese oxidation in caves
- 7.4 Remaining Questions about Manganese Oxidation in Caves
- 8. Microbial Diversity and Ecology of Lava Caves
- 8.1 Introduction
- 8.2 Geology and Ecology of Lava Caves
- 8.2.1 Physical conditions
- 8.3 Microbiological Studies in Lava Caves
- 8.3.1 Lava cave microorganisms
- 8.4 Eukaryotic Microorganisms
- 8.4.1 Fungi
- 8.4.2 Protozoa and algae
- 8.5 Bacteria and Archaea
- 8.5.1 Methods
- 8.5.2 Microbes in volcanic environments
- 8.5.3 Effects of mat color on microbial diversity
- 8.5.4 Impact of location on microbial diversity
- 8.5.5 Microbial endemism
- 8.5.6 Other lava cave microbiology
- 8.5.7 Nitrogen cycling
- 8.6 Human Impacts and Conservation
- 8.7 MicrobialMorphologies
- 8.7.1 Microbialmats
- 8.7.2 Microbes masquerading as minerals
- 8.8 Astrobiology
- 8.8.1 Life detection strategies
- 8.9 Conclusions and Future Opportunities
- 9. Predicting bacterial diversity in caves associated with sulfuric acid speleogenesis
- 9.1 Introduction
- 9.2 Compilation of Bacterial Diversity Data
- 9.3 Controls on Bacterial Diversity in Sulfidic Karst
- 9.4 Predicting the Distribution of Sulfur Bacteria in Sulfidic Karst
- 9.5 Conclusions
- 10. Microbial Life in Unusual Cave Ecosystems Sustained by Chemosynthetic Primary Production
- 10.1 Introduction
- 10.2 Cave Formation and Features
- 10.2.1 Movile Cave
- 10.2.2 Ayyalon Cave
- 10.3 Microbial Life in a Chemolithoautotrophic Ecosystem
- 10.3.1 Methanotrophy and methylotrophy
- 10.3.2 Microbial metabolism of sulfur
- 10.3.3 Nitrogen cycling
- 10.4 Current Research and Future Perspectives
- 10.4.1 Isolates and whole genome sequence analysis
- 10.4.2 Microbial community composition analysis using metagenome sequences
- 10.4.3 Archaeal communities
- 10.5 Conclusions
- 11. The Microbiology of Show Caves, Mines, Tunnels, and Tombs: Implications for Management and Conservation
- 11.1 Introduction
- 11.2 Major Groups of Microorganisms
- 11.2.1 Archaea
- 11.2.2 Bacteria
- 11.2.3 Fungi
- 11.3 Consequences of Microbial Growth and Biogeochemical Cycling
- 11.4 Cave Management
- 12. The Diversity and Ecology of Microbes Associated with Lampenflora in Cave and Karst Settings
- 12.1 Introduction
- 12.2 Photosynthesis and Artificial Lighting
- 12.3 Species Composition
- 12.4 Transport of Lampenflora Species and Their Relevance Underground
- 12.5 Survival Strategies of Phototrophs
- 12.6 Colonization of Solid Surfaces
- 12.7 Biodeterioration and Remediation
- 12.8 Conclusions
- 13. Lascaux Cave: An Example of Fragile Ecological Balance in Subterranean Environments
- 13.1 Introduction
- 13.2 Review of Historical Events, Conservation Efforts, and Scientific Research
- 13.2.1 Discovery and public exhibition
- 13.2.2 First microbial crisis (1955-1970)
- 13.2.3 Returning to the microbial balance (1970-2001)
- 13.2.4 Second microbial crisis (2001-2006)
- 13.2.5 Third microbial crisis (2006-Present)
- 13.3 Recent Research on the Black Stains Outbreak (2009-2013)
- 13.3.1 Ochroconis associated with the black stains
- 13.3.2 Evaluation of biocide treatment of black stains on limestone
- 13.3.3 Black stain fungal communities on clayey sediment
- 13.3.4 Origin of the black stains on clayey sediments
- 13.4 Conclusions
- 14. Scientific Data Suggest Altamira Cave Should Remain Closed
- 14.1 Introduction
- 14.2 History
- 14.3 Altamira Cave Environmental Conditions
- 14.4 Altamira Cave Since 2009
- 14.4.1 Yellow colonies
- 14.4.2 Gray colonies
- 14.4.3 White colonies
- 14.5 Fungi in Altamira Cave
- 14.6 Why Should Altamira Cave Remain Closed?
- 14.7 Final Remarks
- Index
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