Genomic and evolutionary comparisons of diazotrophic and pathogenic bacteria of the order Rhizobiales

Abstract

Background: Species belonging to the Rhizobiales are intriguing and extensively researched for including both bacteria with the ability to fix nitrogen when in symbiosis with leguminous plants and pathogenic bacteria to animals and plants. Similarities between the strategies adopted by pathogenic and symbiotic Rhizobiales have been described, as well as high variability related to events of horizontal gene transfer. Although it is well known that chromosomal rearrangements, mutations and horizontal gene transfer influence the dynamics of bacterial genomes, in Rhizobiales, the scenario that determine pathogenic or symbiotic lifestyle are not clear and there are very few studies of comparative genomic between these classes of prokaryotic microorganisms trying to delineate the evolutionary characterization of symbiosis and pathogenesis.

Results: Non-symbiotic nitrogen-fixing bacteria and bacteria involved in bioremediation closer to symbionts and pathogens in study may assist in the origin and ancestry genes and the gene flow occurring in Rhizobiales. The genomic comparisons of 19 species of Rhizobiales, including nitrogen-fixing, bioremediators and pathogens resulted in 33 common clusters to biological nitrogen fixation and pathogenesis, 15 clusters exclusive to all nitrogen-fixing bacteria and bacteria involved in bioremediation, 13 clusters found in only some nitrogen-fixing and bioremediation bacteria, 01 cluster exclusive to some symbionts, and 01 cluster found only in some pathogens analyzed. In BBH performed to all strains studied, 77 common genes were obtained, 17 of which were related to biological nitrogen fixation and pathogenesis. Phylogenetic reconstructions for Fix, Nif, Nod, Vir, and Trb showed possible horizontal gene transfer events, grouping species of different phenotypes.

Conclusions: The presence of symbiotic and virulence genes in both pathogens and symbionts does not seem to be the only determinant factor for lifestyle evolution in these microorganisms, although they may act in common stages of host infection. The phylogenetic analysis for many distinct operons involved in these processes emphasizes the relevance of horizontal gene transfer events in the symbiotic and pathogenic similarity.

Figure 1

Phylogeny model reconstructed with 104 housekeeping concatenated proteins of representatives of the Rhizobiales order. Phylogeny model reconstructed with 104 housekeeping concatenated proteins of 30 strains (belonging to 25 species) of the order Rhizobiales. The Neighbor-Joining method was applied with Phylip 3.67 program and 1,000 replicates for bootstrap support. Representatives of the beta-Proteobacteria class were used as the outgroup. The 19 strains selected for the comparative analyses in this study are highlighted (Rhizobium sp. NGR234 is not included in this tree because its complete genome is not available).

Figure 2

Representation of the clusters obtained in BBH for biological nitrogen fixation, bioremediation, and pathogenesis processes. Representation of the clusters obtained in BBH for each biological process. (A) BBH between symbiotic and non-symbiotic nitrogen-fixing bacteria and between nitrogen-fixing and bioremediation bacteria; (B) BBH between pathogenic bacteria; (C) the common and exclusives clusters analyzed in nitrogen-fixing bacteria, bacteria involved in bioremediation and pathogenic bacteria BBHs. (A)(B): * number of the clusters analyzed, total 96 clusters. (C): * repeat clusters obtained for NifS and FixQ. They are considered as unique NifS and unique FixQ in the analysis. (C): ** FixK was also identified in the BBH between nitrogen-fixing bacteria, but this cluster was not considered common for the bacterial analyzed because the cluster contained only one FixK present in R. tumefaciens. However, this protein was included in the FixK nitrogen-fixing cluster in phylogeny and presence and absence genes table. (C): *** Other clusters related to evolution mechanisms (not analyzed in detail).

Figure 3

FixNOP, FixABC, TrbCFGIJ and FixS phylogenies. Phylogenies of selected nitrogen fixation and conjugation proteins obtained by BBH, reconstructed with the Neighbor-Joining method of the Phylip 3.67 program, with 1,000 replicates for bootstrap support. (A) concatenated phylogeny for FixNOP proteins; (B) concatenated phylogeny for FixABC proteins; (C) phylogeny for FixS protein; (D) concatenated phylogeny for TrbCFGIJ proteins.

Figure 4

NodN and NodD phylogenies. Phylogenies of selected nodulation proteins obtained by BBH, reconstructed with the Neighbor-Joining method of the Phylip 3.67 program, with 1,000 replicates for bootstrap support. (A) phylogeny for NodN protein; (B) NodD protein.

Figure 5

VirB 8 and VirB9 phylogenies. Phylogenies of selected proteins of type IV secretion system obtained by BBH reconstructed with the Neighbor-Joining method of the Phylip 3.67 program, with 1,000 replicates for bootstrap support. (A) phylogeny for VirB8 protein; (B) VirB9 protein.

Figure 6

Horizontal gene transfers in the evolution of Fix, Nod, Vir, and Trb proteins in Rhizobiales. Model of the horizontal gene transfer events occurring to Fix, Nod, Vir, and Trb proteins in the Rhizobiales species studied.

Figure 7

Genomic location and the synteny to fix-nif genes of the Rhizobiales. Genomic location and the synteny to fix-nif genes analyzed in the Rhizobiales species studied.

Figure 8

Genomic location and the synteny to nod, and vir genes of the Rhizobiales. Genomic location and the synteny to nod (A), and vir (B) genes analyzed in the Rhizobiales species studied.

Figure 9

Genomic location and the synteny to tra- trb genes of the Rhizobiales. Genomic location and the synteny to tra-trb genes analyzed in the Rhizobiales species studied.