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Background   Burkholderia  species play an important ecological role related to xenobiosis, the promotion of plant growth, the biocontrol of agricultural diseases, and symbiotic and non-symbiotic biological nitrogen fixation. Here, we highlight our study as providing the first complete genome of a symbiotic strain of  B. phenoliruptrix , BR3459a (=CLA1), which was originally isolated in Brazil from nodules of  Mimosa flocculosa  and is effective in fixing nitrogen in association with this leguminous species.    Results  Genomic comparisons with other pathogenic and non-pathogenic  Burkholderia  strains grouped  B. phenoliruptrix  BR3459a with plant-associated beneficial and environmental species, although it shares a high percentage of its gene repertoire with species of the  B. cepacia  complex (Bcc) and "pseudomallei" group. The genomic analyses showed that the  bce  genes involved in exopolysaccharide production are clustered together in the same genomic region, constituting part of the Group III cluster of non-pathogenic bacteria. Regarding environmental stresses, we highlight genes that might be relevant in responses to osmotic, heat, cold and general stresses. Furthermore, a number of particularly interesting genes involved in the machinery of the T1SS, T2SS, T3SS, T4ASS and T6SS secretion systems were identified. The xenobiotic properties of strain BR3459a were also investigated, and some enzymes involved in the degradation of styrene, nitrotoluene, dioxin, chlorocyclohexane, chlorobenzene and caprolactam were identified. The genomic analyses also revealed a large number of antibiotic-related genes, the most important of which were correlated with streptomycin and novobiocin. The symbiotic plasmid showed high sequence identity with the symbiotic plasmid of  B. phymatum . Additionally, comparative analysis of 545 housekeeping genes among pathogenic and non-pathogenic  Burkholderia  species strongly supports the definition of a new genus for the second branch, which would include BR3459a.    Conclusions  The analyses of  B. phenoliruptrix  BR3459a showed key property of fixing nitrogen that together with genes for high tolerance to environmental stresses might explain a successful strategy of symbiosis in the tropics. The strain also harbours interesting sets of genes with biotechnological potential. However, the resemblance of certain genes to those of pathogenic  Burkholderia  raise concerns about large-scale applications in agriculture or for bioremediation.    Electronic supplementary material  The online version of this article (doi:10.1186/1471-2164-15-535) contains supplementary material, which is available to authorized users.

bmc genomics

The complete genome of Burkholderia phenoliruptrix strain BR3459a, a symbiont of Mimosa flocculosa: highlighting the coexistence of symbiotic and pathogenic genes