Table of Contents

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 Aquatic Environments 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 Modern Stromatolites 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 Springs Reveals Phylogenetic Relationships and Host Co-Evolution 45
Thomas W. Schoenfeld and David Mead

7. Next-Generation Sequencing and Metagenomic Analysis: A Universal Diagnostic Tool in Plant Pathology 63
Ian P. Adams, Rachel H. Glover, Wendy A. Monger, Richard Thwaites, Rick Mumford, Elena Jackeviciene, Meletele Navalinskiene, Marija Samuitiene, and Neil Boonham

8. Direct Metagenomic Detection of Viral Pathogens in Human Specimens Using an Unbiased High-Throughput Sequencing Approach 73
Takaaki Nakaya, Shota Nakamura, Yoshiko Okamoto, Yoshiyuki Nagai, Jun Kawai, Yoshihide Hayashizaki, Tetsuya Iida, and Toshihiro Horii

Part 2 The Soil Habitat

9. Soil-Based Metagenomics 83
Rolf Daniel

10. Methods in Metagenomic DNA, RNA, and Protein Isolation from Soil 93
T. Rajesh, J. Rajendhran, P. Lavanya Pushpam, and P. Gunasekaran

11. Soil Microbial DNA Purification Strategies for Multiple Metagenomic Applications 109
Larissa C. Parsley, Chengcang Wu, David Mead, Robert M. Goodman, and Mark R. Liles

12. Application of PCR-DGGE and MetagenomeWalking to Retrieve Full-Length Functional Genes from Soil 117
Sho Morimoto and Takeshi Fujii

13. Actinobacterial Diversity Associated with Antarctic Dry Valley 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 Using Large-Insert Metagenomic
Approaches 135
Anna M. Kielak and George A. Kowalchuk

15. Novelty and Uniqueness Patterns of Rare Members of the Soil Biosphere 143
Mostafa S. Elshahed and Noha H. Youssef

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 151
Sergio E. Morales, Theodore F. Cosart, Jesse V. Johnson, and William E. Holben

17. The Antibiotic Resistome: Origins, Diversity, and Future Prospects 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. de Vos, Erwin G. Zoetendal, and Michiel Kleerebezem

19. Assessment and Improvement of Methods for Microbial DNA Preparation 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 Diseases 199
Johan Dicksved and Ben Willing

21. Culture-Independent Analysis of the Human Gut Microbiota and their Activities 207
Jonathan Swann, Selena E. Richards, Qing Shen, Elaine Holmes, Julian R. Marchesi, and Kieran Tuohy

22. Complete Genome of an Uncultured Endosymbiont Coupling Nitrogen Fixation to Cellulolysis within Protist Cells in Termite Gut 221
Yuichi Hongoh

23. Cloning and Identification of Genes Encoding Acidic Cellulases 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 a Seasonally Anoxic Fjord: Saanich Inlet, British Columbia 253
David A. Walsh and Steven J. Hallam

26. Adaptation to Nutrient Availability in Marine Microorganisms by Gene Gain and Loss 269
Adam C. Martiny, Ying Huang, and Weizhong Li

27. Detection of Large Numbers of Novel Sequences in the Metatranscriptomes of Complex Marine Microbial Communities 277
Jack A. Gilbert, Dawn Field, Ying Huang, Robert A. Edwards, Weizhong Li, Paul Gilna, and Ian Joint

28. Metagenomic Approach Studying the Taxonomic and Functional Diversity of the Bacterial Community in a Lacustrine Ecosystem 287
Didier Debroas, Fran¸cois Enault, Isabelle Jouan-Dufournel, Gis`ele Bronner, and Jean-Fran¸cois Humbert

29. Metagenomics of the Marine Subsurface: The First Glimpse from 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, and David J. Scanlan

31. Diversity and Role of Bacterial Integron/Gene Cassette Metagenome 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 Microbial Consortium of a Gutless Marine Worm 321
Manuel Kleiner, Tanja Woyke, Caroline Ruehland, and Nicole Dubilier

33. Microbiome Diversity in Human Saliva 335
Ivan Nasidze and Mark Stoneking

34. Approaches to Understanding Population Level Functional Diversity in a Microbial Community 341
Devaki Bhaya

35. A Functional Metagenomic Approach for Discovering Nickel Resistance Genes from the Rhizosphere of an Acid Mine Drainage Environment 355
Salvador Mirete, Carolina G. de Figueras, and Jose E. Gonz´alez-Pastor

36. The Microbiome of Leaf-Cutter Ant Fungus Gardens 367
Garret Suen, Jarrod J. Scott, Frank O. Aylward, and Cameron R. Currie

37. Diversity of Archaea in Terrestrial Hot Springs and Role in Ammonia Oxidation 381
Chuanlun L. Zhang, Brian P. Hedlund, and Jun Meng

38. Colonization of Nascent, Deep-Sea Hydrothermal Vents by a Novel Archaeal and Nanoarchaeal Assemblage 395
Thomas D. Niederberger, Elizabeth A. McCliment, and S. Craig Cary

39. Analysis of the Metagenome from a Biogas-Producing Microbial Community by Means of Bioinformatics Methods 403
Sebastian Jaenicke, Martha Zakrzewski, Sebastian J¨unemann, Alfred P¨uhler, Alexander Goesmann, and Andreas Schl¨uter

40. Amplicon Pyrosequencing Analysis of Endosymbiont Population Structure 415
Frank J. Stewart and Colleen M. Cavanaugh

41. Investigating Bacterial Diversity Along Alkaline Hot-Spring Thermal Gradients by Barcoded Pyrosequencing 423
Scott R. Miller and Michael Weltzer

42. Genetic Characterization of Microbial Communities Living at the Surface of Building Stones 429
Ma¨ıt´e Berdoulay and Jean-Claude Salvado

Part 6 Biodegradation

43. Novel Aromatic Degradation Pathway Genes and their Organization as Revealed by
Metagenomic Analysis 439
Kentaro Miyazaki

44. Functional Screening a Wide Host-Range Metagenomic Library from a Wastewater
Treatment Plant Yields a Novel Alcohol/Aldehyde Dehydrogenase 451
Margaret Wexler, Philip L. Bond, David J. Richardson, and Andrew W. B. Johnston

45. Aromatic Hydrocarbon Degradation Genes from Chronically Polluted Subantarctic
Marine Sediments 461
Hebe M. Dionisi, Mariana Lozada, Magal´ı S. Marcos, Walter D. Di Marzio, and Claudia L. Loviso

46. Isolation and Characterization of Alkane Hydroxylases from 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 Its Industrial Relevance: Overcoming Limitations and Redirecting the Search 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, and Wolfgang R. Streit

49. Expanding Small-Molecule Functional Metagenomics through Parallel Screening of Broad Host-Range Cosmid Environmental DNA Libraries in Diverse Proteobacteria 507
Jeffrey W. Craig and Sean F. Brady

50. Biomedicinals from the Microbial Metagenomes of Marine Invertebrates 517
Walter C. Dunlap, Paul F. Long, and Marcel Jaspars

51. Molecular Characterization of TEM-Type Beta-Lactamases Identified in Cold-Seep Sediments of Edison Seamount (South of Lihir Island, Papua New Guinea) 545
Sang Hee Lee and Jung-Hyun Lee

52. Identification of Novel Bioactive Compounds from the Metagenome of the Marine  Sponge Haliclona simulans 553
David P. H. Lejon, Jonathan Kennedy, and Alan D. W. Dobson

53. Functional Viral Metagenomics and the Development of New Enzymes for DNA
and RNA Amplification and Sequencing 563
Thomas W. Schoenfeld, Nick Hermersmann, Mike Moser, Darby Renneckar, Vinay Dhodda, and David Mead

Part 8 Summary

54. Metagenomics: The Paths Forward 581
C. Titus Brown and James M. Tiedje

55. Darwin in the Twenty-First Century: Natural Selection, Molecular Biology, and Species Concepts 589
Francisco J. Ayala

Index 597

About the Author

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.

Reviews

Handbook of Molecular MicrobialEcology II is an invaluable reference for researchers inmetagenomics, microbial ecology, microbiology; those working on theHuman Microbiome Project; microbial geneticists; and professionalsin molecular microbiology and bioinformatics. (Bois etForets des Tropiques, 2011)