Microbial Life of Cave Systems

Name: Microbial Life of Cave Systems
Brand: De Gruyter
Price: 189.95 EUR
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Annette Summers Engel(Editor)

De Gruyter (Publisher)

1st Edition

Published on 16. October 2015

XV, 335 pages

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978-3-11-033988-8 (ISBN)

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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
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Microbial Life of Cave Systems

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