Microbes are extremely diverse, yet only a tiny fraction of organisms present in any given environment can be cultivated in the laboratory. Evaluating microbial diversity and identifying individual organisms responsible for specific processes in the environment are fundamental and challenging tasks in microbial ecology and applied microbiology. This comprehensive, judicious, and useful volume provides a complete overview of methods and approaches to studying microbial diversity. While emphasizing new innovative methods, the book also addresses established methods and provides “hands on” advice on how to isolate, cultivate, and study organisms.
Depending on the scope of a study, there are many different ways to assess the diversity of bacteria, fungi, and protists. This volume examines the variety of these approaches—and their advantages and drawbacks. From direct measurements of physical, chemical, and biological aspects of the environment to a wide array of molecular tools such as metagenomic and metaproteomic approaches, this volume thoroughly covers the range of assessment possibilities. It also details innovative methods such as the use of genetic information from environmental samples, enrichment cultures, and single cells. Additionally, the book offers practical, essential advice on how to put these methods into practice both within and outside of the laboratory environment.
Key Features
· Provides a comprehensive overview and discusses the latest developments in the field
· Details various innovative methods for assessment of microbes both within and outside of the laboratory
· Reviews many different methods used in microbial ecology and environmental microbiology
· Presents chapters authored by world-renowned experts in the field
· Highlights various aspects of assessing microorganism from the environment
· Includes all aspects of microbial diversity from bacteria and fungi to protists
· Presents a crucial “how to” guide for isolating organisms from different environments
Table of Contents
Part I. Introduction
1. Does Cultivation Still Matter? Karsten Zengler
2. The Human Intestinal Microbiota and Its Impact on Human Health, Mirjana Rajiliæ-Stojanoviæ, Willem M. de Vos, and Erwin G. Zoetendal
Part II. The Status Quo: Who Is Out There? How To Determine Microbial Diversity
3. The Uncountables, William T. Sloan, Christopher Quince, and Thomas P. Curtis
4. The Missing Fungi: New Insights from Culture-Independent Molecular Studies of Soil, S. K. Schmidt, K. L. Wilson, A. F. Meyer, C. W. Schadt, T. M. Porter, and J. M. Moncalvo
5. The Diversity of Free-Living Protists Seen and Unseen, Cultured and Uncultured, David A. Caron and Rebecca J. Gast
6. Microbial Biogeography: Patterns in Microbial Diversity across Space and Time, Noah Fierer
7. The Least Common Denominator: Species or Operational Taxonomic Units? Ramon Rosselló-Mora and Arantxa López-López
8. Measuring Diversity, Jed A. Fuhrman
9. Metagenomics as a Tool To Study Biodiversity, Karen E. Nelson
Part III. Are Microorganisms Nonculturable or not yet Culturable?
10. New Cultivation Strategies for Terrestrial Microorganisms, Peter H. Janssen
11. Cultivation of Marine Symbiotic Microorganisms, Todd A. Ciche
12. Methods To Study Consortia and Mixed Cultures, Boran Kartal and Marc Strous
Part IV. Do We Have To Change Gear? New Cultivation Approaches and New Molecular Approaches Combined
13. Microbial Cell Individuality, Simon V. Avery
14. Nanomechanical Methods To Study Single Cells, Ramya Desikan, Laurene Tetard, Ali Passian, Ram Datar, and Thomas Thundat
15. Single-Cell Genomics, Martin Keller, Christopher W. Schadt, and Anthony V. Palumbo
16. How Many Genes Does a Cell Need? Hamilton O. Smith, John I. Glass, Clyde A. Hutchison III, and J. Craig Venter