Review Symbiosis within Symbiosis: Evolving Nitrogen-[5_TD$DIFF]Fixing Legume Symbionts Philippe Remigi, 1,2,3 Jun Zhu, 4,5 J. Peter W. Young, 6 and Catherine Masson-Boivin 1,2, * Bacterial accessory genes are genomic symbionts with an evolutionary history and future that is different from that of their hosts. Packages of accessory genes move from strain to strain and confer important adaptations, such [7_TD$DIFF]as interaction with eukaryotes. The ability to fix nitrogen with legumes is a remarkable example of a complex trait spread by horizontal transfer of a few key symbiotic genes, converting soil bacteria into legume symbionts. Rhizobia belong to hundreds of species restricted to a dozen genera of the Alphaproteobacteria and Betapro- teobacteria, suggesting infrequent successful transfer between genera but frequent successful transfer within genera. Here we review the genetic and environmental conditions and selective forces that have shaped evolution of this complex symbiotic trait. Spreading Symbiotic Traits: The Possible and the Actual Bacterial genomes are made up of two parts that can be compared to the operating system and applications of a computer. The core genome, shared by all members of a species, encodes functions that are always needed, while the accessory genome, which varies in composition among strains within the species, comprises packages of genes that confer functions that are useful in certain circumstances, such as antibiotic resistance, access to new resources, or interaction with eukaryotic hosts. These accessory packages are readily transferred within and between species, so their evolutionary history is different from that of the core genome, and the selective forces that maintain them are therefore different. In this review, we are concerned with a remarkable example of a complex trait spread by horizontal gene transfer (HGT) of a few key genes [1] that convert soil bacteria into legume symbionts, called rhizobia. These genes encode a signal that unlocks the development of nodules on the roots of compatible legume plants in nitrogen-deficient conditions, and allows the bacteria to enter the nodules and develop into a form that fixes nitrogen for the benefit of the plant (Box 1). The nodule provides a protected niche and abundant nutrition for the bacteria, which can escape in large numbers when the nodule senesces, so the symbiosis benefits both the plant and the bacteria. The bacteria become symbionts of the plant, but the package of symbiosis genes can also be thought of as a symbiont within the bacterial genome – hence, a symbiosis within a symbiosis. We are concerned here with the evolutionary interactions of the three components – plant, bacterium, and symbiosis genes – and in particular with the interplay between these accessory genes and their bacterial core genome. We believe that this example can inform our general understanding of the relationship between the accessory and core components of bacterial genomes. Symbiosis genes have become established in many different bacterial genera, and this diversity is likely to have been key to the evolutionary success of the rhizobium–legume symbiosis, which Trends Nitrogen fixation in symbiosis with legumes involves hundreds of genes, yet rhizobia arose through horizontal transfer of a few essential genes. These nod–nif genes have spread in many taxons during evolution so that rhizobia currently belong to a dozen genera of the Alphaproteobacteria and Betaproteobacteria. Recent data suggest a two-scale dispersion of key symbiotic genes: colonizing a new genus is rare and requires recipient genome modifica- tions, whereas expanding within rhizo- bial genera is frequent and allows symbiovar emergence. The ecological success of the transfer is enhanced by the strong selection the plant exerts towards efficient nodula- tion and infection, and the action of error-prone DNA polymerases that accelerate adaptation to symbiosis after horizontal gene transfer (HGT). Rhizobia can behave as parasites (not nitrogen-fixing), and emergence and maintenance of mutualism may rely on antagonistic co-evolution. 1 INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet-Tolosan, France 2 CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, Castanet-Tolosan, France 3 New Zealand Institute for Advanced Study, Massey University, Auckland, New Zealand 4 Department of Microbiology, Nanjing Agricultural University, Nanjing, China TIMI 1255 No. of Pages 13 Trends in Microbiology, Month Year, Vol. xx, No. yy http://dx.doi.org/10.1016/j.tim.2015.10.007 1 © 2015 Elsevier Ltd. All rights reserved.