Genome characteristics of facultatively symbiotic Frankia sp. strains reflect host range and host plant biogeography

Abstract

Soil bacteria that also form mutualistic symbioses in plants encounter two major levels of selection. One occurs during adaptation to and survival in soil, and the other occurs in concert with host plant speciation and adaptation. Actinobacteria from the genus Frankia are facultative symbionts that form N(2)-fixing root nodules on diverse and globally distributed angiosperms in the "actinorhizal" symbioses. Three closely related clades of Frankia sp. strains are recognized; members of each clade infect a subset of plants from among eight angiosperm families. We sequenced the genomes from three strains; their sizes varied from 5.43 Mbp for a narrow host range strain (Frankia sp. strain HFPCcI3) to 7.50 Mbp for a medium host range strain (Frankia alni strain ACN14a) to 9.04 Mbp for a broad host range strain (Frankia sp. strain EAN1pec.) This size divergence is the largest yet reported for such closely related soil bacteria (97.8%-98.9% identity of 16S rRNA genes). The extent of gene deletion, duplication, and acquisition is in concert with the biogeographic history of the symbioses and host plant speciation. Host plant isolation favored genome contraction, whereas host plant diversification favored genome expansion. The results support the idea that major genome expansions as well as reductions can occur in facultative symbiotic soil bacteria as they respond to new environments in the context of their symbioses.

Figure 1.

Neighbor-joining (Saitou and Nei 1987) phylogenetic tree calculated with ClustalX 1.83 (Thompson et al. 1997) from 16S rRNA gene sequences. Distances were corrected for multiple substitutions (Kimura 1980); otherwise, default settings were used. Numbers give bootstrap support values from 1000 bootstrapped samples. The outgroup used is Streptomyces coelicolor (NC003888). Accession numbers for the organisms are given after the name and species number as given in Normand and Fernandez (2007). In the case of the unisolated cluster 2 frankiae, the host plant genus from which 16S rRNA gene sequences were amplified is given. Distances in the bar are in substitutions/site.

Figure 2.

Present-day native distribution of actinorhizal plant hosts. (A) Distribution of plant hosts for CcI3, including Casuarina and Allocasuarina of the Casuarinaceae (C). (B) Distribution of plant hosts for ACN, including Alnus sp. in the Betulaceae (B) and Myricaceae (M) and their overlap (M+B). (C) Distribution of plant hosts for EAN including members of the Elaeagnaceae (E), Myricaceae (M), and the actinorhizal Tribe Colletieae of the Rhamnaceae in South America, Australia, and New Zealand (R). Elaeagnaceae and Myriceae (E+M) overlap in some areas. Maps were drawn with information from Silvester (1977) and from the Missouri Botanical Garden Web site (www.mobot.org).

Figure 3.

Genome maps of the three Frankia strains. Circles, from the outside in, show (1) gene regions related to symbiosis including shc1, hup2, hup1, and nif; (2) the coordinates in Mb beginning at 0 = oriC; (3) regions of synteny (syntons) calculated as a minimum of five contiguous genes present in all strains with an identity >30% over 80% of the length of the shortest gene (syntons are tagged with a spectrum-based [red-yellow-green] color code standardized on ACN to indicate regions where syntons have moved in the other strains); (4) IS elements and transposases. Circles were drawn using GenVision Software from DNAStar.