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Handbook of Molecular Microbial Ecology II
Metagenomics in Different Habitats
Hardcover | 30 September 2011 | Edition Number 1
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632 Pages
28.7 x 22.86 x 3.4
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"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)
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¨?t´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´? 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
ISBN: 9780470647196
ISBN-10: 0470647191
Published: 30th September 2011
Format: Hardcover
Language: English
Number of Pages: 632
Audience: Professional and Scholarly
Publisher: John Wiley & Sons Inc (US)
Country of Publication: US
Edition Number: 1
Dimensions (cm): 28.7 x 22.86 x 3.4
Weight (kg): 1.94
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