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.