in proper proportions and arrangements, and different replication systems and population genetic processes applicable to different parts of the metagenome. In the following, I consider some of the most prominent symbioses in microorganisms and then focus on the role of symbiosis in generating phenotypic complexity in animals.
Although conventional views of bacteriophage have emphasized their role in killing bacterial hosts, it is now apparent that they often affect host ecology in other, more beneficial ways, including acting as vectors of genes that can enhance bacterial fitness in a particular environment (Comeau and Krisch, 2005; Hendrix, 2002). This realization comes in part from genome sequences for bacteria, which reveal that bacteriophage have made large ongoing contributions to bacterial genome contents and physiological capabilities, often sometimes becoming lasting parts of the bacterial genome even when genes required for the bacteriophage life cycle have been eliminated (Comeau and Krisch, 2005). The richest reservoir of gene diversity lies in the bacteriophage (e.g., Breitbart et al., 2002; Kwan et al., 2005), suggesting that the innovations that they are able to contribute are correspondingly diverse. For example, a very large proportion of pathogenic bacteria studied in humans and other mammals use pathogenicity mechanisms encoded by phage-borne genes (Wagner and Waldor, 2002), some of the competitive mechanisms used among bacterial strains are derived from phage-derived structures (e.g., Nakayama et al., 2000), and the central enzyme components underlying photosynthesis in ubiquitous marine cyanobacteria are transferred among bacterial hosts by bacteriophage (Lindell et al., 2004). Even phage-induced lysis of the bacterial host cell can be a mechanism favoring the growth and fitness of the bacterial host clone, as other cells containing the same phage genes persist and benefit from products released during the death of their sister cells (Wagner and Waldor, 2002).
One consequence of the fact that gene transfer is not without limits even in prokaryotes is the frequent evolution of microbial consortia or microbial syntrophy, that is, close, often obligate, associations of two (or a few) unrelated organisms that depend on one another for metabolic products or maintenance of chemically permissive conditions. Examples of close, coevolved associations include those between methanogenic archaea and bacteria or protists capable of fermentation (e.g., Schink,