Transcriptomic insights into mechanisms of symbiotic cooperation

Intraspecific genetic variation can affect community structure and ecosystem processes (Bolnick et al . 2011). It can also influence phenotypic expression by genotypes within other species to produce genotype‐by‐genotype ( G  ×  G ) interaction (Falconer & Mackay 1996). Evolution of one species drives correlated evolution of others when it causes G  ×  G for fitness (Thompson 2005). However, the mechanisms by which species interact also influence evolutionary outcomes (Kummel & Salant 2006; Golubski & Klausmeier 2010; Akçay & Simms 2011; Grman et al . 2012). To identify genes and putative functional mechanisms underlying G  ×  G interactions, Heath et al . (2012) analysed natural variation in the symbiotic transcriptome of the mutualistic nutritional symbiosis between a legume host M edicago truncatula and the facultative endosymbiotic rhizobium S inorhizobium meliloti . Using twelve microarrays, the authors simultaneously measured host and symbiont gene expression in root nodules from four factorial pairings of host and symbiont genotypes that produced G  ×  G in host fitness (Fig. 1, upper panel). Rhizobium gene expression was influenced by rhizobium and plant genotype and the G  ×  G interaction (Fig. 1, lower panel), whereas plant gene expression was influenced primarily by plant genotype. The authors identified rhizobium genes that might contribute to G  ×  G in host plant fitness. Heath et al . (2012) have moved beyond the constraints of single organism analysis towards a more realistic understanding of plants and bacteria as organisms inextricably linked with symbioses that affect even basic patterns of gene expression.