2002), phototrophic aquatic consortia consisting of a flagellated bacterium coated with phototrophic bacteria (Overmann and Schubert, 2002; Glaeser and Overmann, 2004), and an archaean–bacterium partnership that links methane oxidation and denitrification (Raghoebarsing et al., 2006). More broadly, metabolic interdependencies among lineages are a major reason that most microbes in soil and other natural habitats cannot be established in pure laboratory culture (Schmidt, 2006). In some systems, detailed knowledge of the interactions of the different bacterial types shows that there has been extensive coadaptation, with recognition mechanisms for promoting the associations and with communication systems for coordinating the behavior of cells from phylogenetically distant groups (Schink, 2002).
Molecular phylogenetics, based on sequence data from only a few genes, verified the hypothesis that mitochondria and plastids are derived from bacterial symbionts; these results also identified the bacterial lineages that gave rise to these symbionts and indicated a single primary origin in each case (Woese, 1987; Keeling, 2004; Embley and Martin, 2006; Kurland et al., 2006). Genomic data indicate that both plastids and mitochondria have transferred genes from the bacterial to the host genome, resulting in a genomic mélange (e.g., Martin et al., 2002; Keeling, 2004). Genome sequences have also helped to elucidate further complexities of the mitochondrial and plastid symbioses in some lineages: for example, secondary and tertiary symbioses in which a plastid-containing eukaryote itself becomes a symbiont in a new eukaryotic host, sometimes resulting in bizarre remnant genomes (e.g., Gilson et al., 2006) and complicated histories of gene transfers among several genomes (Keeling, 2004). Beyond cellular organelles, symbioses have arisen innumerable times in eukaryotic hosts. Protists often carry prokaryotic symbionts, and their nuclear genomes may have taken up genes from past symbionts (e.g., Eichinger et al., 2005; Andersson et al., 2005). Much of the complexity of modern eukaryotic cells arises from this divided ancestry involving gene movement between genomes and the evolution of mechanisms for targeting gene products to the correct cellular compartment. Even individual enzymatic pathways or functional systems can be encoded by complex combinations of genes with different histories of direct horizontal transfer, transfer through symbiosis, or vertical inheritance (e.g., Chen et al., 2006; Richards et al., 2006).
Symbioses originating in multicellular eukaryotes are rampant, with highly specialized obligate associations found in fungi, plants, sponges,