Comparative Genomics of Aeschynomene Symbionts: Insights into the Ecological Lifestyle of Nod-Independent Photosynthetic Bradyrhizobia

Damien Mornico, Lucie Miché, Gilles Béna, Nico Nouwen, André Verméglio, David Vallenet, Alexander A.T. Smith, Eric Giraud, Claudine Médigue, Lionel Moulin
2011 Genes  
Tropical aquatic species of the legume genus Aeschynomene are stem-and root-nodulated by bradyrhizobia strains that exhibit atypical features such as photosynthetic capacities or the use of a nod gene-dependent (ND) or a nod gene-independent (NI) pathway to enter into symbiosis with legumes. In this study we used a comparative genomics approach on nine Aeschynomene symbionts representative of their phylogenetic diversity. We produced draft genomes of bradyrhizobial strains representing
more » ... phenotypes: five NI photosynthetic strains (STM3809, ORS375, STM3847, STM4509 and STM4523) in addition to the previously sequenced ORS278 and BTAi1 genomes, one photosynthetic strain ORS285 hosting both ND and NI symbiotic systems, and one NI non-photosynthetic strain (STM3843). Comparative genomics allowed us to infer the core, OPEN ACCESS Genes 2012, 3 36 pan and dispensable genomes of Aeschynomene bradyrhizobia, and to detect specific genes and their location in Genomic Islands (GI). Specific gene sets linked to photosynthetic and NI/ND abilities were identified, and are currently being studied in functional analyses. Introduction Rhizobia are soil bacteria able to develop nitrogen-fixing symbioses with legumes, by the formation of organ-like structures on plant roots called nodules. Following differentiation into bacteroids, they transform atmospheric dinitrogen into ammonium that they provide to the plant in exchange for carbohydrates. Rhizobia are polyphyletic and spread among the classes Alphaproteobacteria and Betaproteobacteria [1] . Bradyrhizobium is a genus within alphaproteobacteria comprising many symbiotic species phylogenetically spread into three main clades: the B. japonicum clade, the B. elkanii clade and the photosynthetic Bradyrhizobium (PB) clade [2, 3] . The photosynthetic bradyrhizobia clade is composed of symbionts specific to the tropical Aeschynomene legume species, on which they form root but also stem nodules. Stem nodulation is a plant-dependent ability quite unusual in legumes, described in only five genera (Aeschynomene, Discolobium, Neptunia, Sesbania and Vigna) and is often associated to the plants' aquatic life in wet or temporarily flooded habitats [4, 5] . The infection process in Sesbania rostrata and Aeschynomene species during water-stress conditions occurs by "crack entry" (a process different from root hair curling) by intercellular infection of epidermal fissures (cracks) generated by the emergence of lateral roots [6, 7] . The nodulation process between Sesbania rostrata and its specific symbiont Azorhizobium caulinodans occurs via a classic Nod-factor dependent process [7, 8] . The symbiotic interaction between Aeschynomene and photosynthetic Bradyrhizobium, however, presents several particularities. First, by definition, PB possess a photosynthetic activity [9] that might play a role in symbiosis, either by conferring a selective advantage for bacterial survival ex planta (as a supplementary source of energy), and/or by facilitating bacterial infectivity and symbiotic effectiveness [10, 11] . Second, some photosynthetic bradyrhizobia lack the canonical nodulation genes (genome-based analyses on ORS278 and BTAi1) and use an unknown nod gene-independent pathway to form nodules on some Aeschynomene species [12, 13] . Aeschynomene species are categorized into three cross-inoculation (CI) groups [14, 15] , linked to specific features of their symbionts mentioned above: their photosynthetic ability, their capacity to form stem nodules, and finally their use of a nod gene-dependent (ND) or nod gene-independent (NI) symbiotic pathway. The CI group I includes Aeschynomene species nodulated only on their roots by non-photosynthetic bradyrhizobia, stem nodulation being restricted to CI group 2 and 3. CI group 3 is characterized by plant species nodulated only by PB lacking nodulation (nod) genes (NI, as strains ORS278 and BTAi1 symbiotic of A. indica and A. sensitiva), while CI group 2 species are nodulated by both photosynthetic and non-photosynthetic strains (as A. afraspera) [14] . It is relevant to note that photosynthetic strains able to nodulate CI group 2 (as ORS285) nodulate also CI group 3, as they carry both the ND and NI systems. Indeed an isogenic nodA minus mutant of ORS285 lost its symbiotic ability on CI group 2 but was still able to nodulate efficiently CI group 3 [13]. In a
doi:10.3390/genes3010035 pmid:24704842 pmcid:PMC3899966 fatcat:stztth6c2bccdormmua4jawco4