Preface xiii Contributors xv 1. Introduction 1 Frans J. de Bruijn Part 1 Viral Genomes 2. Viral Metagenomics 5 Shannon J. Williamson 3. Methods in Viral Metagenomics 15 Rebecca Vega Thurber 4. Metagenomic Contrasts of Viruses in Soil and AquaticEnvironments 25 K. Eric Wommack, Sharath Srinivasiah, Mark R.
Liles,Jaysheel Bhavsar, Shellie Bench, Kurt E. Williamson, and Shawn W.Polson 5. Biodiversity and Biogeography of Phages in ModernStromatolites and Thrombolites 37 Christelle 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 Rohwer 6. Assembly of Viral Metagenomes from Yellowstone Hot SpringsReveals Phylogenetic Relationships and Host Co-Evolution 45 Thomas W. Schoenfeld and David Mead 7. Next-Generation Sequencing and Metagenomic Analysis: AUniversal Diagnostic Tool in Plant Pathology 63 Ian P. Adams, Rachel H. Glover, Wendy A. Monger, RichardThwaites, Rick Mumford, Elena Jackeviciene, Meletele Navalinskiene,Marija Samuitiene, and Neil Boonham 8. Direct Metagenomic Detection of Viral Pathogens in HumanSpecimens Using an Unbiased High-Throughput Sequencing Approach73 Takaaki Nakaya, Shota Nakamura, Yoshiko Okamoto, YoshiyukiNagai, Jun Kawai, Yoshihide Hayashizaki, Tetsuya Iida, andToshihiro Horii Part 2 The Soil Habitat 9.
Soil-Based Metagenomics 83 Rolf Daniel 10. Methods in Metagenomic DNA, RNA, and Protein Isolationfrom Soil 93 T. Rajesh, J. Rajendhran, P. Lavanya Pushpam, and P.Gunasekaran 11. Soil Microbial DNA Purification Strategies for MultipleMetagenomic Applications 109 Larissa C. Parsley, Chengcang Wu, David Mead, Robert M.
Goodman, and Mark R. Liles 12. Application of PCR-DGGE and MetagenomeWalking to RetrieveFull-Length Functional Genes from Soil 117 Sho Morimoto and Takeshi Fujii 13. Actinobacterial Diversity Associated with Antarctic DryValley Mineral Soils 125 Bronwyn M. Kirby, Marilize Le Roes-Hill, S. Craig Cary,Stephanie G. Burton, I. Marla Tuffin, and Don A.
Cowan 14. Targeting Major Soil-Borne Bacterial Lineages UsingLarge-Insert Metagenomic Approaches 135 Anna M. Kielak and George A. Kowalchuk 15. Novelty and Uniqueness Patterns of Rare Members of theSoil Biosphere 143 Mostafa S. Elshahed and Noha H. Youssef 16. Extensive Phylogenetic Analysis of a Soil BacterialCommunity Illustrates Extreme Taxon Evenness and the Effects ofAmplicon Length, Degree of Coverage, and DNA Fractionation onClassification and Ecological Parameters 151 Sergio E.
Morales, Theodore F. Cosart, Jesse V. Johnson, andWilliam E. Holben 17. The Antibiotic Resistome: Origins, Diversity, and FutureProspects 165 Erin L.Westman and Gerard D.Wright Part 3 The Digestive Tract 18. Functional Intestinal Metagenomics 177 Bartholomeus van den Bogert, Milkha M.
Leimena, Willem M. deVos, Erwin G. Zoetendal, and Michiel Kleerebezem 19. Assessment and Improvement of Methods for Microbial DNAPreparation from Fecal Samples 191 Mariko Ueno, Mami Kikuchi, Kenshiro Oshima, Seok-won Kim,Hidetoshi Morita, and Masahira Hattori 20. The Role of Dysbiosis in Inflammatory Bowel Diseases199 Johan Dicksved and Ben Willing 21. Culture-Independent Analysis of the Human Gut Microbiotaand their Activities 207 Jonathan Swann, Selena E. Richards, Qing Shen, ElaineHolmes, Julian R. Marchesi, and Kieran Tuohy 22.
Complete Genome of an Uncultured Endosymbiont CouplingNitrogen Fixation to Cellulolysis within Protist Cells in TermiteGut 221 Yuichi Hongoh 23. Cloning and Identification of Genes Encoding AcidicCellulases from the Metagenomes of Buffalo Rumen 229 Cheng-Jie Duan, Jun-Liang Liu, and Jia-Xun Feng Part 4 Marines and Lakes 24. Microbial Diversity in the Deep Sea and the Underexplored?Rare Biosphere? 245 David B. Mark Welch and Susan M. Huse 25. Bacterial Community Structure and Dynamics in aSeasonally Anoxic Fjord: Saanich Inlet, British Columbia 253 David A. Walsh and Steven J. Hallam 26.
Adaptation to Nutrient Availability in MarineMicroorganisms by Gene Gain and Loss 269 Adam C. Martiny, Ying Huang, and Weizhong Li 27. Detection of Large Numbers of Novel Sequences in theMetatranscriptomes of Complex Marine Microbial Communities277 Jack A. Gilbert, Dawn Field, Ying Huang, Robert A. Edwards,Weizhong Li, Paul Gilna, and Ian Joint 28. Metagenomic Approach Studying the Taxonomic andFunctional Diversity of the Bacterial Community in a LacustrineEcosystem 287 Didier Debroas, Fran¸cois Enault, IsabelleJouan-Dufournel, Gis'ele Bronner, and Jean-Fran¸coisHumbert 29. Metagenomics of the Marine Subsurface: The First Glimpsefrom the Peru Margin, ODP Site 1229 295 Jennifer F. Biddle 30.
A Targeted Metagenomic Approach to Determine the?Population Genome? of Marine Synechococcus 301 Sophie Mazard, Martin Ostrowski, Laurence Garczarek, andDavid J. Scanlan 31. Diversity and Role of Bacterial Integron/Gene CassetteMetagenome in Extreme Marine Environments 309 Hosam Elsaied and Akihiko Maruyama Part 5 Other Habitats 32. The Olavius algarvensis Metagenome Revisited:Lessons Learned from the Analysis of the Low-Diversity MicrobialConsortium of a Gutless Marine Worm 321 Manuel Kleiner, Tanja Woyke, Caroline Ruehland, and NicoleDubilier 33. Microbiome Diversity in Human Saliva 335 Ivan Nasidze and Mark Stoneking 34. Approaches to Understanding Population Level FunctionalDiversity in a Microbial Community 341 Devaki Bhaya 35. A Functional Metagenomic Approach for Discovering NickelResistance Genes from the Rhizosphere of an Acid Mine DrainageEnvironment 355 Salvador Mirete, Carolina G. de Figueras, and Jose E.
Gonz´alez-Pastor 36. The Microbiome of Leaf-Cutter Ant Fungus Gardens367 Garret Suen, Jarrod J. Scott, Frank O. Aylward, and CameronR. Currie 37. Diversity of Archaea in Terrestrial Hot Springs and Rolein Ammonia Oxidation 381 Chuanlun L. Zhang, Brian P. Hedlund, and Jun Meng 38.
Colonization of Nascent, Deep-Sea Hydrothermal Vents by aNovel Archaeal and Nanoarchaeal Assemblage 395 Thomas D. Niederberger, Elizabeth A. McCliment, and S. CraigCary 39. Analysis of the Metagenome from a Biogas-ProducingMicrobial Community by Means of Bioinformatics Methods 403 Sebastian Jaenicke, Martha Zakrzewski, SebastianJ¨unemann, Alfred P¨uhler, Alexander Goesmann, andAndreas Schl¨uter 40. Amplicon Pyrosequencing Analysis of EndosymbiontPopulation Structure 415 Frank J. Stewart and Colleen M. Cavanaugh 41.
Investigating Bacterial Diversity Along AlkalineHot-Spring Thermal Gradients by Barcoded Pyrosequencing 423 Scott R. Miller and Michael Weltzer 42. Genetic Characterization of Microbial Communities Livingat the Surface of Building Stones 429 Ma¨?t´e Berdoulay and Jean-ClaudeSalvado Part 6 Biodegradation 43. Novel Aromatic Degradation Pathway Genes and theirOrganization as Revealed by Metagenomic Analysis 439 Kentaro Miyazaki 44. Functional Screening a Wide Host-Range MetagenomicLibrary from a Wastewater Treatment Plant Yields a Novel Alcohol/Aldehyde Dehydrogenase451 Margaret Wexler, Philip L. Bond, David J. Richardson, andAndrew W. B.
Johnston 45. Aromatic Hydrocarbon Degradation Genes from ChronicallyPolluted Subantarctic Marine Sediments 461 Hebe M. Dionisi, Mariana Lozada, Magal´? S.Marcos, Walter D. Di Marzio, and Claudia L. Loviso 46. Isolation and Characterization of Alkane Hydroxylasesfrom a Metagenomic Library of Pacific Deep-Sea Sediment 475 Fengping Wang, Meixiang Xu, and Xiang Xiao Part 7 Biocatalysts and Natural Products 47. Emerging Fields in Functional Metagenomics and ItsIndustrial Relevance: Overcoming Limitations and Redirecting theSearch for Novel Biocatalysts 483 Mirjam Perner, Nele Ilmberger, Hans Ulrich K¨ohler,Jennifer Chow, and Wolfgang R.
Streit 48. Carboxylesterases and Lipases from Metagenomes 499 Jennifer Chow, Ulrich Krauss, Karl-Erich Jaeger, andWolfgang R. Streit 49. Expanding Small-Molecule Functional Metagenomics throughParallel Screening of Broad Host-Range Cosmid Environmental DNALibraries in Diverse Proteobacteria 507 Jeffrey W. Craig and Sean F. Brady 50. Biomedicinals from the Microbial Metagenomes of MarineInvertebrates 517 Walter C. Dunlap, Paul F.
Long, and Marcel Jaspars 51. Molecular Characterization of TEM-Type Beta-LactamasesIdentified in Cold-Seep Sediments of Edison Seamount (South ofLihir Island, Papua New Guinea) 545 Sang Hee Lee and Jung-Hyun Lee 52. Identification of Novel Bioactive Compounds from theMetagenome of the Marine.