lineages have evolved diverse mechanisms to gain entry and proliferate in the tissues and cells of multicellular eukaryotes (Merhej et al., 2009; Carvalho et al., 2010; Medina and Sachs, 2010; Toft and Andersson, 2010), and these symbionts vary in their effect on hosts from harmful to beneficial (Medina and Sachs, 2010; Toft and Andersson, 2010). Archaea have also evolved associations with hosts, but these interactions do not appear as diverse or ubiquitous. Bacterial symbioses (defined in the broad sense) include persistent, intimate associations between bacteria and other species and date back at least to the origins of eukaryotes (Sagan, 1967). Bacterial parasites range from infectious diseases that rapidly exploit hosts before infecting new individuals, to bacteria that are transmitted vertically from host parent to offspring and manipulate host reproduction to favor their own spread (Stouthamer et al., 1999). Parasitic bacteria have received intense focus from researchers over the last century because harmful infections represent a critical challenge to human health and economic interests. In contrast, except for a few early pioneers (Buchner, 1921), researchers have only recently focused on the biology of bacteria that enhance host fitness: bacterial mutualists (Sachs et al., 2011).
Bacterial mutualists are diverse (Williams et al., 2007, 2010; Merhej et al., 2009; Wu et al., 2009; Carvalho et al., 2010; Medina and Sachs, 2010; Philippot et al., 2010; Toft and Andersson, 2010) and exhibit a variety of lifestyles and coevolutionary relationships with eukaryote hosts (Sachs et al., 2011) (Table 2.1). First, beneficial bacteria vary in their degree of reliance on hosts for reproduction. Whereas some bacterial-derived organelles and endosymbionts cannot live independently of hosts, most bacterial mutualists retain extensive environmental phases and form infections that are facultative for the bacterium (Szathmáry and Smith, 1995; Nyholm and McFall-Ngai, 2004; Sachs et al., 2011). Second, bacterial mutualists inhabit diverse host tissues ranging from skin, mucosa, leaves, and roots to inter- and intracellular spaces. Some bacterial mutualists inhabit specialized structures in hosts (Becking, 1970; Savage, 1977; Sprent et al., 1987; Douglas, 1989; Bright and Sorgo, 2003; Currie et al., 2006; Nussbaumer et al., 2006; Visick and Ruby, 2006; Goettler et al., 2007; Vaishnava et al., 2008; Pflugfelder et al., 2009; Ran et al., 2010), whereas others range widely in host mucosa or other unstructured tissues (Hirose, 2000; Hirose et al., 2009; Kaltenpoth et al., 2009) (Table 2.1). Finally, bacterial mutualists provide a great variety of benefits to hosts, including nutrients (Becking, 1970; Sprent et al., 1987; Douglas, 1989; Hirose, 2000; Hooper et al., 2002; Ran et al., 2010), bioluminescence (Nyholm and McFall-Ngai, 2004), and antibiotic production (Currie et al., 1999; Kaltenpoth et al., 2005; Kost et al., 2007). Although bacterial mutualists by definition provide a net fitness benefit to hosts,