Preface. Contributors. 1. Introduction (Frans J. de Bruijn). Viral Genomes. 2. Viral metagenomics (Shannon Williamson). 3. Methods in Viral Metagenomics (Thurber). 4. Metagenomic contrasts of viruses in soil and aquatic environments (Eric Wommack). 5. Biodiversity and biogeography of phages in modern stromatolites and thromolites (Christelle Desnues). 6. Assembly of Viral Metagenomes from Yellowstone Hot Springs Reveals Phylogenetic Relationships and Host Co-Evolution (Thomas Schoenfeld). 7. Next-generation sequencing and metagenomic analysis; a universal diagnostic tool in plant pathology (Ian Adams). 8. Direct Metagenomic Detection of Viral Pathogens in Human Specimens Using an Unbiased High-throughput Sequencing Approach (T. Nakaya). The Soil Habitat. 9. Soil based Metagenomics (R. Daniel). 10. Methods in Metagenomic DNA, RNA and Protein Isolation from Soil (P. Gunasharan). 11. Soil Microbial DNA Purification Strategies for Multiple Metagenomic Applications (Mark Liles). 12. Application of PCR-DGGE and metagenome walking to retrieve full-length functional genes from soil (Morimoto). 13. Actinobacterial diversity associated with Antarctic Dry Valley mineral soils (Cowan). 14. Targetting major soil-borne bacterial lineages using large-insert metaenomic approaches (G. Kowalchuk). 15. Novelty and uniqueness patterns of rare members of the soil biosphere (M. Elshahed). 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 (Holben WE). 17. The Antibiotic Resistance: Origins, Diversity, and Future Prospects (Gerard Wright). The Digestive Tract. 18. Functional Intestinal Metagenomics (Michael Kleerebezem). 19. Assessment and improvement of methods for microbial DNA preparation from fecal Samples (M. Hattori). 20. Role of dysbiosis in inflammatory bowel diseases (Johan Dicksved). 21. Culture independent analysis of the human gut microbiota and its activities (Kieran Tuohi). 22. Complete genome of an uncultured endowsymbiont coupling nitrogen fixation to cellulolysis with protest cells in termite gut (Hongo). 23. Cloning and identification of genes encoding acidic cellulases from metagenomes of buffalo rumen (Feng). Marine and Lakes. 24. Microbial diversity in the deep seas and the underexplored "rare biosphere" (David Mark Welsch and Susan Huse). 25. Bacterial Community Structure and Dynamics in a Seasonally Anoxic Fjord (Steven J. Hallam). 26. Adaptation to nutrient availability in marine microorganisms by gene gain and loss (A. Martini). 27. Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities (Jack Gilbert). 28. Metagenomic approach studying the taxonomic and functional diversity of the bacterial community in a lacustrine ecosystem (Didier Debroas). 29. Metagenomics of the marine subsurface: the first glimpse from the Peru Margin, ODP Site 122 (Jennifer Biddle). 30. A targeted metagenomic approach to determine the 'population genome' of marine Synechoccus (D. J. Scanlan). 31. Diversity and role of bacterial integron/gene cassette metagenome in extreme marine environments (Hosam Easa Elsaied and Akihiko Maruyama). Other Habitats. 32. The Olavius algarvensis metagenome revisited: lessons learned from the analysis of the low diversity microbial consortium of a gutless marine worm(Nicole Dubulier). 33. Microbiome diversity in human saliva (Ivan Nasidze). 34. Approaches to understanding population level functional diversity in a microbial community (D. Bhaya). 35. A functional metagenomic approach for discovering nickel resistance genes from the rhizosphere of an acid mine drainage environment (JOSE Gonzales -Pastor). 36. The Microbiome of Leaf-cutter Ant Fungus Gardens (Garret Suen). 37. Diversity of archaea in terrestrial hot springs and role In ammonia oxidation (Chuanlun Zhang). 38. Colinization of nascent, deep-sea hydrothermal vents by a novel Archaeal and Nanoarchaeal assemblage (S. Craig Cary). 39. Analysis of the Metagenome from a biogas-producing microbial Community by means of Bioinformatucs Methods (Andreas Schlueter). 40. Amplicon pyrosequencing analysis of endosymbiont population structure (Colleen Kavahagh). 41. Investigative bacterial diversity along alkaline hot spring thermal gradients by barcoded pyrosequencing (Scott Miller and Michael Welzer). 42. Genetic characterization of microbial communities living at the surface of building stones (J. C. Salvado). 43. Novel aromatic degradation pathway genes and their organization as revealed by metagenomic analysis (Kentaro). 44. Functional screening of a wide host-range metagenomic library from a wastewater treatment plant yields a novel alcohol/aldehyde dehydrogenase (Wexler). 45. Aromatic hydrocarbon degradation genes from chronically polluted Subantarctic marine sediments (H. M. Dionisi). 46. Isolation and characterization if alkane hydroxylases from a metagenomic llibrary of Pacific deep-sea sediment (Fengping Wang). Biocatalysts and Natural Products. 47. Emerging Fields in Functional Metagenomics and its Industrial Relevance - Overcoming Limitations and Redirecting the Search for Novel Biocatalysts (Wolfgang Streit). 48. Carboxylesterases and Lipases from Metagenomes (Chow and Wolfgang Streit). 49. Expanding small molecule functional megenomics through parallel screening of broad host-range cosmid environmental DNA libraries in diverse Proteobacteria (Sean Brady). 50. Biomedicinals from the microbial metagenomes of marine invertebrates (Walter Dunlap). 51. Molecular characterization of TEM-type beta-Lactamases identified in Cold-seep sediments of Edison Seamount (South of Lihir Island). 52. Identification of Novel Bioactive Compounds from the Metagenome of the Marine (David Lejon). 53. Functional Viral Metagenomics and the Development of New Enzymes for DNA and RNA Amplification and Sequencing (Thomas Schoenfeld). Summary. 54. Future of metagenomics, metatranscriptomics, metabolomics, metaproteomics and single cell analysis: A perspective (J. Tiedje). 55. Darwin in the 21st Century: Natural Selection, Molecular Biology, and Species Concepts (Francisco Ayala).