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2 - Bacteriophages: models for exploring basic principles of ecology
- from Part I - Phage ecology
- Edited by Stephen T. Abedon, Ohio State University
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- Book:
- Bacteriophage Ecology
- Published online:
- 29 September 2009
- Print publication:
- 01 May 2008, pp 31-63
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Summary
INTRODUCTION
A virus depends intimately upon its host in order to reproduce, which makes the host organism a crucial part of the virus's environment. This basic facet of viral existence means that ecology, the scientific field focusing on how organisms interact with each other and their environment, is particularly relevant to the study of viruses. In this chapter we explore some of the ways in which the principles of ecology apply to viruses that infect bacteria — the bacteriophages (or “phages” for short). In turn, we also discuss how the study of phages and their bacterial hosts has contributed to different subfields of ecology.
Due to their ease of manipulation, large population sizes, short generation times, and wealth of physiological and genetic characterization, laboratory communities of microbial organisms have been popular experimental tools for testing ecological theory (Drake et al., 1996; Jessup et al., 2004). Building upon this foundation of knowledge, the ecological experimentalist can explore whether mechanistic understanding at the organismal level informs an understanding of patterns at the community level (Bohannan and Lenski, 2000a). Further, the initial composition of microbial consortia can be controlled, and thus researchers are able to probe the effects of different community structures on ecological phenomena, such as stability, diversity, and resilience to invasion.
7 - Biodiversity scaling relationships: are microorganisms fundamentally different?
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- By Jessica Green, University of California, Merced, Brendan J. M. Bohannan, University of Oregon
- Edited by David Storch, Charles University, Prague, Pablo Marquet, Pontificia Universidad Catolica de Chile, James Brown, University of New Mexico
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- Book:
- Scaling Biodiversity
- Published online:
- 05 August 2012
- Print publication:
- 12 July 2007, pp 129-149
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Summary
Introduction
One of the key goals of ecology is to understand the spatial scaling of species diversity. Spatial patterns of species diversity provide important clues about the underlying mechanisms that regulate biodiversity and are central in the development of biodiversity theory (MacArthur & Wilson, 1967; Rosenzweig, 1995; Brown, 1995; Gaston & Blackburn, 2000; Hubbell, 2001; Holyoak, Leibold & Holt, 2005). Assumptions regarding the spatial scaling of biodiversity are a fundamental component of conservation biology and are frequently used to identify local- and global-scale priority conservation areas (Ferrier et al., 2004; Desmet & Cowling, 2004) and to predict extinction risk due to climate change (Thomas et al., 2004) and habitat loss (Gaston, Blackburn & Goldewijk, 2003). Although scaling patterns have been documented in hundreds of studies of plant and animal diversity, such patterns in microbial species (i.e. bacteria, archaea, and single-celled eukarya) have not been well documented. This is a serious omission, given that microorganisms may comprise much of Earth's biodiversity (Whitman, Coleman & Wiebe, 1998; Torsvik, Ovreas & Thingstad, 2002) and play critical roles in biogeochemical cycling and ecosystem functioning (Balser, 2000; Wardle, 2002; Morin & McGrady-Steed, 2004). Furthermore, microbial biodiversity is a major source of novel pharmaceuticals and other compounds of industrial importance, and an understanding of the scaling of microbial biodiversity is crucial to the search for such compounds (Bull, 2004).
Patterns in prokaryotic biodiversity
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- By M. Claire Horner-Devine, School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA 98195, USA, Jessica Green, School of Natural Sciences, University of California, Merced, CA 95344, USA, Brendan J. M. Bohannan, Department of Biological Sciences, Stanford University, Stanford, CA 94305, USA
- Edited by N. A. Logan, Glasgow Caledonian University, H. M. Lappin-Scott, University of Exeter, P. C. F Oyston, Defence Science and Technology Laboratory, Porton Down
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- Book:
- Prokaryotic Diversity
- Published online:
- 06 July 2010
- Print publication:
- 20 April 2006, pp 19-38
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Summary
INTRODUCTION
The variety of life has long fascinated biologists. One of the most intriguing aspects of this diversity is that it is distributed heterogeneously across the Earth, with some places harbouring a myriad of different forms of life and others supporting depauperate communities. There appear to be regularities in this heterogeneous distribution, patterns in the distribution of life's diversity, for many well-studied macro-organisms. Until recently, relatively few patterns in the distribution of microbial life have been documented, in large part because microbiologists and ecologists have just recently begun to look for such patterns.
Diversity patterns have played a major role in the development of the science of general ecology (i.e. theoretical, plant, animal and ecosystem ecology). It is reasonable to assume that the study of diversity patterns could play a similar role in the development of microbial ecology. Where should one look for such patterns in microbial biodiversity? Given our limited knowledge of the distribution of microbial diversity, it is reasonable to start by looking for patterns in microbial diversity that are commonly observed for macro-organisms. In this chapter, we begin by discussing how diversity in general and microbial diversity in particular is estimated. We then describe a number of diversity patterns commonly observed for macro-organisms and review recent attempts to document such patterns in microbial diversity. We focus primarily on prokaryotic micro-organisms; however, patterns in the diversity of eukaryotic microbes have also been documented (e.g. Green et al., 2004; Smith et al., 2005).