Details

Handbook of Molecular Microbial Ecology II

Metagenomics in Different Habitats
1. Aufl.

von: Frans J. de Bruijn
289,99 €
Verlag:	Wiley-Blackwell
Format:	PDF
Veröffentl.:	01.06.2011
ISBN/EAN:	9781118010525
Sprache:	englisch
Anzahl Seiten:	600

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Titelbeschreibung

The premiere two-volume reference on revelations from studying complex microbial communities in many distinct habitats Metagenomics is an emerging field that has changed the way microbiologists study microorganisms. It involves the genomic analysis of microorganisms by extraction and cloning of DNA from a group of microorganisms, or the direct use of the purified DNA or RNA for sequencing, which allows scientists to bypass the usual protocol of isolating and culturing individual microbial species. This method is now used in laboratories across the globe to study microorganism diversity and for isolating novel medical and industrial compounds. Handbook of Molecular Microbial Ecology is the first comprehensive two-volume reference to cover unculturable microorganisms in a large variety of habitats, which could not previously have been analyzed without metagenomic methodology. It features review articles as well as a large number of case studies, based largely on original publications and written by international experts. This second volume, Metagenomics in Different Habitats, covers such topics as: <ul> <li> Viral genomes </li> <li> Metagenomics studies in a variety of habitats, including marine environments and lakes, soil, and human and animal digestive tracts </li> <li> Other habitats, including those involving microbiome diversity in human saliva and functional intestinal metagenomics; diversity of archaea in terrestrial hot springs; and microbial communities living at the surface of building stones </li> <li> Biodegradation </li> <li> Biocatalysts and natural products </li> </ul> A special feature of this book is the highlighting of the databases and computer programs used in each study; they are listed along with their sites in order to facilitate the computer-assisted analysis of the vast amount of data generated by metagenomic studies. Such studies in a variety of habitats are described here, which present a large number of different system-dependent approaches in greatly differing habitats. Handbook of Molecular Microbial Ecology II is an invaluable reference for researchers in metagenomics, microbial ecology, microbiology, and environmental microbiology; those working on the Human Microbiome Project; microbial geneticists; and professionals in molecular microbiology and bioinformatics.

Inhaltsverzeichnis

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

Rezension

"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)

Autorenportrait

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.

Back cover copy

The premiere two-volume reference on revelations from studying complex microbial communities in many distinct habitats Metagenomics is an emerging field that has changed the way microbiologists study microorganisms. It involves the genomic analysis of microorganisms by extraction and cloning of DNA from a group of microorganisms, or the direct use of the purified DNA or RNA for sequencing, which allows scientists to bypass the usual protocol of isolating and culturing individual microbial species. This method is now used in laboratories across the globe to study microorganism diversity and for isolating novel medical and industrial compounds. Handbook of Molecular Microbial Ecology is the first comprehensive two-volume reference to cover unculturable microorganisms in a large variety of habitats, which could not previously have been analyzed without metagenomic methodology. It features review articles as well as a large number of case studies, based largely on original publications and written by international experts. This second volume, Metagenomics in Different Habitats, covers such topics as: <ul> <li> Viral genomes </li> <li> Metagenomics studies in a variety of habitats, including marine environments and lakes, soil, and human and animal digestive tracts </li> <li> Other habitats, including those involving microbiome diversity in human saliva and functional intestinal metagenomics; diversity of archaea in terrestrial hot springs; and microbial communities living at the surface of building stones </li> <li> Biodegradation </li> <li> Biocatalysts and natural products </li> </ul> A special feature of this book is the highlighting of the databases and computer programs used in each study; they are listed along with their sites in order to facilitate the computer-assisted analysis of the vast amount of data generated by metagenomic studies. Such studies in a variety of habitats are described here, which present a large number of different system-dependent approaches in greatly differing habitats. Handbook of Molecular Microbial Ecology II is an invaluable reference for researchers in metagenomics, microbial ecology, microbiology, and environmental microbiology; those working on the Human Microbiome Project; microbial geneticists; and professionals in molecular microbiology and bioinformatics.