Handbook of Molecular Microbial Ecology II Metagenomics in Different Habitats 1st Edition by Frans de Bruijn 0470647191 9780470647196

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ISBN 10: 0470647191

ISBN 13: 9780470647196

Author: Frans J. de Bruijn

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:

• Viral genomes
• Metagenomics studies in a variety of habitats, including marine environments and lakes, soil, and human and animal digestive tracts
• 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
• Biodegradation
• Biocatalysts and natural products

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.

Table of contents:

1. Introduction
Frans J. de Bruijn

Part 1 Viral Genomes

2. Viral Metagenomics
   Shannon J. Williamson

3. Methods in Viral Metagenomics
   Rebecca Vega Thurber

4. Metagenomic Contrasts of Viruses in Soil and Aquatic Environments
   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
   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
   Thomas W. Schoenfeld and David Mead

7. Next-Generation Sequencing and Metagenomic Analysis: A Universal Diagnostic Tool in Plant Pathology
   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
   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
   Rolf Daniel

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

11. Soil Microbial DNA Purification Strategies for Multiple Metagenomic Applications
    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
    Sho Morimoto and Takeshi Fujii

13. Actinobacterial Diversity Associated with Antarctic Dry Valley Mineral Soils
    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
    Anna M. Kielak and George A. Kowalchuk

15. Novelty and Uniqueness Patterns of Rare Members of the Soil Biosphere
    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
    Sergio E. Morales, Theodore F. Cosart, Jesse V. Johnson, and William E. Holben

17. The Antibiotic Resistome: Origins, Diversity, and Future Prospects
    Erin L. Westman and Gerard D. Wright

Part 3 The Digestive Tract

18. Functional Intestinal Metagenomics
    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
    Mariko Ueno, Mami Kikuchi, Kenshiro Oshima, Seok-won Kim, Hidetoshi Morita, and Masahira Hattori

20. The Role of Dysbiosis in Inflammatory Bowel Diseases
    Johan Dicksved and Ben Willing

21. Culture-Independent Analysis of the Human Gut Microbiota and their Activities
    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
    Yuichi Hongoh

23. Cloning and Identification of Genes Encoding Acidic Cellulases from the Metagenomes of Buffalo Rumen
    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”
    David B. Mark Welch and Susan M. Huse

25. Bacterial Community Structure and Dynamics in a Seasonally Anoxic Fjord: Saanich Inlet, British Columbia
    David A. Walsh and Steven J. Hallam

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

27. Detection of Large Numbers of Novel Sequences in the Metatranscriptomes of Complex Marine Microbial Communities
    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
    Didier Debroas, François Enault, Isabelle Jouan-Dufournel, Gisèle Bronner, and Jean-François Humbert

29. Metagenomics of the Marine Subsurface: The First Glimpse from the Peru Margin, ODP Site 1229
    Jennifer F. Biddle

30. A Targeted Metagenomic Approach to Determine the “Population Genome” of Marine Synechococcus
    Sophie Mazard, Martin Ostrowski, Laurence Garczarek, and David J. Scanlan

31. Diversity and Role of Bacterial Integron/Gene Cassette Metagenome in Extreme Marine Environments
    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
    Manuel Kleiner, Tanja Woyke, Caroline Ruehland, and Nicole Dubilier

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

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

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

36. The Microbiome of Leaf-Cutter Ant Fungus Gardens
    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
    Chuanlun L. Zhang, Brian P. Hedlund, and Jun Meng

38. Colonization of Nascent, Deep-Sea Hydrothermal Vents by a Novel Archaeal and Nanoarchaeal Assemblage
    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
    Sebastian Jaenicke, Martha Zakrzewski, Sebastian Jünemann, Alfred Pühler, Alexander Goesmann, and Andreas Schlüter

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

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

42. Genetic Characterization of Microbial Communities Living at the Surface of Building Stones
    Maïté Berdoulay and Jean-Claude Salvado

Part 6 Biodegradation

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

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

45. Aromatic Hydrocarbon Degradation Genes from Chronically Polluted Subantarctic Marine Sediments
    Hebe M. Dionisi, Mariana Lozada, Magalí 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
    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
    Mirjam Perner, Nele Ilmberger, Hans Ulrich Köhler, Jennifer Chow, and Wolfgang R. Streit

48. Carboxylesterases and Lipases from Metagenomes
    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
    Jeffrey W. Craig and Sean F. Brady

50. Biomedicinals from the Microbial Metagenomes of Marine Invertebrates
    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)
    Sang Hee Lee and Jung-Hyun Lee

52. Identification of Novel Bioactive Compounds from the Metagenome of the Marine Sponge Haliclona simulans
    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
    Thomas W. Schoenfeld, Nick Hermersmann, Mike Moser, Darby Renneckar, Vinay Dhodda, and David Mead

Part 8 Summary

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

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

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Tags: Frans de Bruijn, Molecular, Microbial, Ecology