Handbook of Molecular Microbial Ecology II

Frans J. de Bruijn received his Ph.D. (Cellular and Developmental Biology; Microbial Genetics) from Harvard University in 1983.? His resume reflects an array of experiences as a teacher, researcher, board member and a plethora of other accomplishments. He is currently?Director of Research at the Laboratory for Plant-Microbe Interactions in Toulouse, France.

• Preface xiii Contributors xv1. Introduction 1Frans J. de BruijnPart 1 Viral Genomes2. Viral Metagenomics 5Shannon J. Williamson3. Methods in Viral Metagenomics 15Rebecca Vega Thurber4. Metagenomic Contrasts of Viruses in Soil and Aquatic Environments 25K. Eric Wommack, Sharath Srinivasiah, Mark R. Liles, Jaysheel Bhavsar, Shellie Bench, Kurt E. Williamson, and Shawn W. Polson5. Biodiversity and Biogeography of Phages in Modern Stromatolites and Thrombolites 37Christelle Desnues, Beltran Rodriguez-Brito, Steve Rayhawk, Scott Kelley, Tuong Tran, Matthew Haynes, Hong Liu, Mike Furlan, Linda Wegley, Betty Chau, Yijun Ruan, Dana Hall, Florent E. Angly, Robert A. Edwards, Linlin Li, Rebecca Vega Thurber, R. Pamela Reid, Janet Siefert, Valeria Souza, David L. Valentine, Brandon K. Swan, Mya Breitbart, and Forest Rohwer6. Assembly of Viral Metagenomes from Yellowstone Hot Springs Reveals Phylogenetic Relationships and Host Co-Evolution 45Thomas W. Schoenfeld and David Mead7. Next-Generation Sequencing and Metagenomic Analysis: A Universal Diagnostic Tool in Plant Pathology 63Ian P. Adams, Rachel H. Glover, Wendy A. Monger, Richard Thwaites, Rick Mumford, Elena Jackeviciene, Meletele Navalinskiene, Marija Samuitiene, and Neil Boonham8. Direct Metagenomic Detection of Viral Pathogens in Human Specimens Using an Unbiased High-Throughput Sequencing Approach 73Takaaki Nakaya, Shota Nakamura, Yoshiko Okamoto, Yoshiyuki Nagai, Jun Kawai, Yoshihide Hayashizaki, Tetsuya Iida, and Toshihiro HoriiPart 2 The Soil Habitat9. Soil-Based Metagenomics 83Rolf Daniel10. Methods in Metagenomic DNA, RNA, and Protein Isolation from Soil 93T. Rajesh, J. Rajendhran, P. Lavanya Pushpam, and P. Gunasekaran11. Soil Microbial DNA Purification Strategies for Multiple Metagenomic Applications 109Larissa C. Parsley, Chengcang Wu, David Mead, Robert M. Goodman, and Mark R. Liles12. Application of PCR-DGGE and MetagenomeWalking to Retrieve Full-Length Functional Genes from Soil 117Sho Morimoto and Takeshi Fujii13. Actinobacterial Diversity Associated with Antarctic Dry Valley Mineral Soils 125Bronwyn M. Kirby, Marilize Le Roes-Hill, S. Craig Cary, Stephanie G. Burton, I. Marla Tuffin, and Don A. Cowan14. Targeting Major Soil-Borne Bacterial Lineages Using Large-Insert MetagenomicApproaches 135Anna M. Kielak and George A. Kowalchuk15. Novelty and Uniqueness Patterns of Rare Members of the Soil Biosphere 143Mostafa S. Elshahed and Noha H. Youssef16. 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 151Sergio E. Morales, Theodore F. Cosart, Jesse V. Johnson, and William E. Holben17. The Antibiotic Resistome: Origins, Diversity, and Future Prospects 165Erin L.Westman and Gerard D.WrightPart 3 The Digestive Tract18. Functional Intestinal Metagenomics 177Bartholomeus van den Bogert, Milkha M. Leimena, Willem M. de Vos, Erwin G. Zoetendal, and Michiel Kleerebezem19. Assessment and Improvement of Methods for Microbial DNA Preparation from Fecal Samples 191Mariko Ueno, Mami Kikuchi, Kenshiro Oshima, Seok-won Kim, Hidetoshi Morita, and Masahira Hattori20. The Role of Dysbiosis in Inflammatory Bowel Diseases 199Johan Dicksved and Ben Willing21. Culture-Independent Analysis of the Human Gut Microbiota and their Activities 207Jonathan Swann, Selena E. Richards, Qing Shen, Elaine Holmes, Julian R. Marchesi, and Kieran Tuohy22. Complete Genome of an Uncultured Endosymbiont Coupling Nitrogen Fixation to Cellulolysis within Protist Cells in Termite Gut 221Yuichi Hongoh23. Cloning and Identification of Genes Encoding Acidic Cellulases from the Metagenomes of Buffalo Rumen 229Cheng-Jie Duan, Jun-Liang Liu, and Jia-Xun FengPart 4 Marines and Lakes24. Microbial Diversity in the Deep Sea and the Underexplored “Rare Biosphere” 245David B. Mark Welch and Susan M. Huse25. Bacterial Community Structure and Dynamics in a Seasonally Anoxic Fjord: Saanich Inlet, British Columbia 253David A. Walsh and Steven J. Hallam26. Adaptation to Nutrient Availability in Marine Microorganisms by Gene Gain and Loss 269Adam C. Martiny, Ying Huang, and Weizhong Li27. Detection of Large Numbers of Novel Sequences in the Metatranscriptomes of Complex Marine Microbial Communities 277Jack A. Gilbert, Dawn Field, Ying Huang, Robert A. Edwards, Weizhong Li, Paul Gilna, and Ian Joint28. Metagenomic Approach Studying the Taxonomic and Functional Diversity of the Bacterial Community in a Lacustrine Ecosystem 287Didier Debroas, Fran¸cois Enault, Isabelle Jouan-Dufournel, Gis`ele Bronner, and Jean-Fran¸cois Humbert29. Metagenomics of the Marine Subsurface: The First Glimpse from the Peru Margin, ODP Site 1229 295Jennifer F. Biddle30. A Targeted Metagenomic Approach to Determine the “Population Genome” of Marine Synechococcus 301Sophie Mazard, Martin Ostrowski, Laurence Garczarek, and David J. Scanlan31. Diversity and Role of Bacterial Integron/Gene Cassette Metagenome in Extreme Marine Environments 309Hosam Elsaied and Akihiko MaruyamaPart 5 Other Habitats32. The Olavius algarvensis Metagenome Revisited: Lessons Learned from the Analysis of the Low-Diversity Microbial Consortium of a Gutless Marine Worm 321Manuel Kleiner, Tanja Woyke, Caroline Ruehland, and Nicole Dubilier33. Microbiome Diversity in Human Saliva 335Ivan Nasidze and Mark Stoneking34. Approaches to Understanding Population Level Functional Diversity in a Microbial Community 341Devaki Bhaya35. A Functional Metagenomic Approach for Discovering Nickel Resistance Genes from the Rhizosphere of an Acid Mine Drainage Environment 355Salvador Mirete, Carolina G. de Figueras, and Jose E. Gonz´alez-Pastor36. The Microbiome of Leaf-Cutter Ant Fungus Gardens 367Garret Suen, Jarrod J. Scott, Frank O. Aylward, and Cameron R. Currie37. Diversity of Archaea in Terrestrial Hot Springs and Role in Ammonia Oxidation 381Chuanlun L. Zhang, Brian P. Hedlund, and Jun Meng38. Colonization of Nascent, Deep-Sea Hydrothermal Vents by a Novel Archaeal and Nanoarchaeal Assemblage 395Thomas D. Niederberger, Elizabeth A. McCliment, and S. Craig Cary39. Analysis of the Metagenome from a Biogas-Producing Microbial Community by Means of Bioinformatics Methods 403Sebastian Jaenicke, Martha Zakrzewski, Sebastian J¨unemann, Alfred P¨uhler, Alexander Goesmann, and Andreas Schl¨uter40. Amplicon Pyrosequencing Analysis of Endosymbiont Population Structure 415Frank J. Stewart and Colleen M. Cavanaugh41. Investigating Bacterial Diversity Along Alkaline Hot-Spring Thermal Gradients by Barcoded Pyrosequencing 423Scott R. Miller and Michael Weltzer42. Genetic Characterization of Microbial Communities Living at the Surface of Building Stones 429Ma¨ıt´e Berdoulay and Jean-Claude SalvadoPart 6 Biodegradation43. Novel Aromatic Degradation Pathway Genes and their Organization as Revealed byMetagenomic Analysis 439Kentaro Miyazaki44. Functional Screening a Wide Host-Range Metagenomic Library from a WastewaterTreatment Plant Yields a Novel Alcohol/Aldehyde Dehydrogenase 451Margaret Wexler, Philip L. Bond, David J. Richardson, and Andrew W. B. Johnston45. Aromatic Hydrocarbon Degradation Genes from Chronically Polluted SubantarcticMarine Sediments 461Hebe M. Dionisi, Mariana Lozada, Magal´ı S. Marcos, Walter D. Di Marzio, and Claudia L. Loviso46. Isolation and Characterization of Alkane Hydroxylases from a Metagenomic Library of Pacific Deep-Sea Sediment 475Fengping Wang, Meixiang Xu, and Xiang XiaoPart 7 Biocatalysts and Natural Products47. Emerging Fields in Functional Metagenomics and Its Industrial Relevance: Overcoming Limitations and Redirecting the Search for Novel Biocatalysts 483Mirjam Perner, Nele Ilmberger, Hans Ulrich K¨ohler, Jennifer Chow, and Wolfgang R. Streit48. Carboxylesterases and Lipases from Metagenomes 499Jennifer Chow, Ulrich Krauss, Karl-Erich Jaeger, and Wolfgang R. Streit49. Expanding Small-Molecule Functional Metagenomics through Parallel Screening of Broad Host-Range Cosmid Environmental DNA Libraries in Diverse Proteobacteria 507Jeffrey W. Craig and Sean F. Brady50. Biomedicinals from the Microbial Metagenomes of Marine Invertebrates 517Walter C. Dunlap, Paul F. Long, and Marcel Jaspars51. Molecular Characterization of TEM-Type Beta-Lactamases Identified in Cold-Seep Sediments of Edison Seamount (South of Lihir Island, Papua New Guinea) 545Sang Hee Lee and Jung-Hyun Lee52. Identification of Novel Bioactive Compounds from the Metagenome of the Marine  Sponge Haliclona simulans 553David P. H. Lejon, Jonathan Kennedy, and Alan D. W. Dobson53. Functional Viral Metagenomics and the Development of New Enzymes for DNAand RNA Amplification and Sequencing 563Thomas W. Schoenfeld, Nick Hermersmann, Mike Moser, Darby Renneckar, Vinay Dhodda, and David MeadPart 8 Summary54. Metagenomics: The Paths Forward 581C. Titus Brown and James M. Tiedje55. Darwin in the Twenty-First Century: Natural Selection, Molecular Biology, and Species Concepts 589Francisco J. AyalaIndex 597

"Handbook of Molecular Microbial Ecology II is an invaluable reference for researchers in metagenomics, microbial ecology, microbiology; those working on the Human Microbiome Project; microbial geneticists; and professionals in molecular microbiology and bioinformatics." (Bois et Forets des Tropiques, 2011)