Plant-bacteria association and symbiosis: are there common genomic traits in alphaproteobacteria?

Abstract

Alphaproteobacteria show a great versatility in adapting to a broad range of environments and lifestyles, with the association between bacteria and plants as one of the most intriguing, spanning from relatively unspecific nonsymbiotic association (as rhizospheric or endophytic strains) to the highly species-specific interaction of rhizobia. To shed some light on possible common genetic features in such a heterogeneous set of plant associations, the genomes of 92 Alphaproteobacteria strains were analyzed with a fuzzy orthologs-species detection approach. This showed that the different habitats and lifestyles of plant-associated bacteria (soil, plant colonizers, symbiont) are partially reflected by the trend to have larger genomes with respect to nonplant-associated species. A relatively large set of genes specific to symbiotic bacteria (73 orthologous groups) was found, with a remarkable presence of regulators, sugar transporters, metabolic enzymes, nodulation genes and several genes with unknown function that could be good candidates for further characterization. Interestingly, 15 orthologous groupspresent in all plant-associated bacteria (symbiotic and nonsymbiotic), but absent in nonplant-associated bacteria, were also found, whose functions were mainly related to regulation of gene expression and electron transport. Two of these orthologous groups were also detected in fully sequenced plant-associated Betaproteobacteria and Gammaproteobacteria. Overall these results lead us to hypothesize that plant-bacteria associations, though quite variable, are partially supported by a conserved set of unsuspected gene functions.

Figure 1

Phylogenetic tree based on 16S rRNA gene sequence for the 92 selected organisms. Names in green and cyan indicate plant-associated species (green, symbionts; cyan, nonsymbionts). The dimension of the circles is proportional to the genome size, while the color of the circles indicates the GC content.

Figure 2

Number of orthologous groups found inside each life-style species list. Circles sizes are not in scale.

Figure 3

Percent distribution of orthologous groups belonging to the different subsets (Core, Plant-Associated and Plant symbionts) among Cluster of Orthologous Groups (COG) categories. Note that each orthologous group can be mapped to more than one category. The list of COG codes is reported in Supplementary Material S3.

Figure 4

Overview of the cellular functions of the Plant Symbionts gene set. Go categories are color coded. Numbers represent orthologous groups (see Supplementary Material S2).

Figure 5

Taxonomic sharing of life-style associated genes. For each taxonomic division (according to NCBI), the proportion of the life-style related orthologous groups having at least one significant hit is shown.