Handbook of Molecular Microbial Ecology II -- Contents -- Preface -- Contributors -- 1. Introduction -- Part 1 Viral Genomes -- 2. Viral Metagenomics -- 3. Methods in Viral Metagenomics -- 4. Metagenomic Contrasts of Viruses in Soil and Aquatic Environments -- 5. Biodiversity and Biogeography of Phages in Modern Stromatolites and Thrombolites -- 6. Assembly of Viral Metagenomes from Yellowstone Hot Springs Reveals Phylogenetic Relationships and Host Co-Evolution -- 7. Next-Generation Sequencing and Metagenomic Analysis: A Universal Diagnostic Tool in Plant Pathology -- 8. Direct Metagenomic Detection of Viral Pathogens in Human Specimens Using an Unbiased High-Throughput Sequencing Approach -- Part 2 The Soil Habitat -- 9. Soil-Based Metagenomics -- 10. Methods in Metagenomic DNA, RNA, and Protein Isolation from Soil -- 11. Soil Microbial DNA Purification Strategies for Multiple Metagenomic Applications -- 12. Application of PCR-DGGE and Metagenome Walking to Retrieve Full-Length Functional Genes from Soil -- 13. Actinobacterial Diversity Associated with Antarctic Dry Valley Mineral Soils -- 14. Targeting Major Soil-Borne Bacterial Lineages Using Large-Insert Metagenomic Approaches -- 15. Novelty and Uniqueness Patterns of Rare Members of the Soil Biosphere -- 16. Extensive Phylogenetic Analysis of a Soil Bacterial Community Illustrates Extreme Taxon Evenness and the Effects of Amplicon Length, Degree of Coverage, and DNA Fractionation on Classification and Ecological Parameters -- 17. The Antibiotic Resistome: Origins, Diversity, and Future Prospects -- Part 3 The Digestive Tract -- 18. Functional Intestinal Metagenomics -- 19. Assessment and Improvement of Methods for Microbial DNA Preparation from Fecal Samples -- 20. The Role of Dysbiosis in Inflammatory Bowel Diseases.

21. Culture-Independent Analysis of the Human Gut Microbiota and their Activities -- 22. Complete Genome of an Uncultured Endosymbiont Coupling Nitrogen Fixation to Cellulolysis within Protist Cells in Termite Gut -- 23. Cloning and Identification of Genes Encoding Acidic Cellulases from the Metagenomes of Buffalo Rumen -- Part 4 Marines and Lakes -- 24. Microbial Diversity in the Deep Sea and the Underexplored "Rare Biosphere" -- 25. Bacterial Community Structure and Dynamics in a Seasonally Anoxic Fjord: Saanich Inlet, British Columbia -- 26. Adaptation to Nutrient Availability in Marine Microorganisms by Gene Gain and Loss -- 27. Detection of Large Numbers of Novel Sequences in the Metatranscriptomes of Complex Marine Microbial Communities -- 28. Metagenomic Approach Studying the Taxonomic and Functional Diversity of the Bacterial Community in a Lacustrine Ecosystem -- 29. Metagenomics of the Marine Subsurface: The First Glimpse from the Peru Margin, ODP Site 1229 -- 30. A Targeted Metagenomic Approach to Determine the "Population Genome" of Marine Synechococcus -- 31. Diversity and Role of Bacterial Integron/Gene Cassette Metagenome in Extreme Marine Environments -- Part 5 Other Habitats -- 32. The Olavius algarvensis Metagenome Revisited: Lessons Learned from the Analysis of the Low-Diversity Microbial Consortium of a Gutless Marine Worm -- 33. Microbiome Diversity in Human Saliva -- 34. Approaches to Understanding Population Level Functional Diversity in a Microbial Community -- 35. A Functional Metagenomic Approach for Discovering Nickel Resistance Genes from the Rhizosphere of an Acid Mine Drainage Environment -- 36. The Microbiome of Leaf-Cutter Ant Fungus Gardens -- 37. Diversity of Archaea in Terrestrial Hot Springs and Role in Ammonia Oxidation.

38. Colonization of Nascent, Deep-Sea Hydrothermal Vents by a Novel Archaeal and Nanoarchaeal Assemblage -- 39. Analysis of the Metagenome from a Biogas-Producing Microbial Community by Means of Bioinformatics Methods -- 40. Amplicon Pyrosequencing Analysis of Endosymbiont Population Structure -- 41. Investigating Bacterial Diversity Along Alkaline Hot-Spring Thermal Gradients by Barcoded Pyrosequencing -- 42. Genetic Characterization of Microbial Communities Living at the Surface of Building Stones -- Part 6 Biodegradation -- 43. Novel Aromatic Degradation Pathway Genes and their Organization as Revealed by Metagenomic Analysis -- 44. Functional Screening a Wide Host-Range Metagenomic Library from a Wastewater Treatment Plant Yields a Novel Alcohol/Aldehyde Dehydrogenase -- 45. Aromatic Hydrocarbon Degradation Genes from Chronically Polluted Subantarctic Marine Sediments -- 46. Isolation and Characterization of Alkane Hydroxylases from a Metagenomic Library of Pacific Deep-Sea Sediment -- Part 7 Biocatalysts and Natural Products -- 47. Emerging Fields in Functional Metagenomics and Its Industrial Relevance: Overcoming Limitations and Redirecting the Search for Novel Biocatalysts -- 48. Carboxylesterases and Lipases from Metagenomes -- 49. Expanding Small-Molecule Functional Metagenomics through Parallel Screening of Broad Host-Range Cosmid Environmental DNA Libraries in Diverse Proteobacteria -- 50. Biomedicinals from the Microbial Metagenomes of Marine Invertebrates -- 51. Molecular Characterization of TEM-Type Beta-Lactamases Identified in Cold-Seep Sediments of Edison Seamount (South of Lihir Island, Papua New Guinea) -- 52. Identification of Novel Bioactive Compounds from the Metagenome of the Marine Sponge Haliclona simulans -- 53. Functional Viral Metagenomics and the Development of New Enzymes for DNA and RNA Amplification and Sequencing.

Part 8 Summary -- 54. Metagenomics: The Paths Forward -- 55. Darwin in the Twenty-First Century: Natural Selection, Molecular Biology, and Species Concepts -- Index.